diff --git a/README.md b/README.md
index 96d6cf043..378fdc8a9 100644
--- a/README.md
+++ b/README.md
@@ -240,6 +240,9 @@ The folder is structured in the following way: Any nonspecific-pangenome file is
       - test_10x_10k_pbmc_cmo_cmo_fastq_\{1,2\}_gz: 3' V3 Cell Multiplexing FASTQs from 10k PBMC data with Cell Multiplexing
       - test_10x_10k_pbmc_cmo_gex\{1,2\}_fastq_\{1,2\}_gz: 3' V3 gene expression FASTQs from 10k PBMC data with Cell Multiplexing
       - test_10x_10k_pbmc_cmo_feature_ref_csv: Feature Barcode reference for the 10k PBMC data with Cell Multiplexing
+      - test_10x_60k_pbmc_cmo_tcr_gex_fastq_\{1,2\}_gz: 5' V2 HT gene expression FASTQs from 60k PBMC data with Cell Multiplexing
+      - test_10x_60k_pbmc_cmo_tcr_ab_fastq_\{1,2\}_gz: 5' V2 HT Feature Barcode & Cell Multiplexing FASTQs from 60k PBMC data (files contain both)
+      - test_10x_60k_pbmc_cmo_tcr_tcr_fastq_\{1,2\}_gz: 5' V2 HT T-cell V(D)J FASTQs from 60k PBMC data with Cell Multiplexing
       - test_10x_5k_cmvpos_tcells_ab_fastq_\{1,2\}_gz: Antibody Capture FASTQs from the 5k CMV+ T-cell dataset
       - test_10x_5k_cmvpos_tcells_gex1_fastq_\{1,2\}_gz: Gene expression FASTQs from the 5k CMV+ T-cell dataset
       - test_10x_5k_cmvpos_tcells_vdj_fastq_\{1,2\}_gz: V(D)J FASTQs from the 5k CMV+ T-cell dataset
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor1_config.csv b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor1_config.csv
new file mode 100644
index 000000000..645265147
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor1_config.csv
@@ -0,0 +1,17 @@
+[gene-expression]
+reference,working-directory/refdata-gex-GRCh38-2020-A/
+force-cells,11638
+check-library-compatibility,false
+
+[feature]
+reference,working-directory/final-analysis/feature_ref.csv
+
+[vdj]
+reference,working-directory/final-analysis/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,working-directory/bamtofastq/Donor1_healthy/demultiplexed_samples_0_1_HW7KMDSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,working-directory/fastqs/ab_fastq,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,working-directory/fastqs/tcr_fastq,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,working-directory/fastqs/bcr_fastq,VDJ-B
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor2_config.csv b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor2_config.csv
new file mode 100644
index 000000000..644b22141
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor2_config.csv
@@ -0,0 +1,17 @@
+[gene-expression]
+reference,working-directory/refdata-gex-GRCh38-2020-A/
+force-cells,8873
+check-library-compatibility,false
+
+[feature]
+reference,working-directory/final-analysis/feature_ref.csv
+
+[vdj]
+reference,working-directory/final-analysis/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,working-directory/bamtofastq/Donor2_healthy/demultiplexed_samples_0_1_HW7KMDSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,working-directory/fastqs/ab_fastq,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,working-directory/fastqs/tcr_fastq,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,working-directory/fastqs/bcr_fastq,VDJ-B
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor3_config.csv b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor3_config.csv
new file mode 100644
index 000000000..367371d1e
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor3_config.csv
@@ -0,0 +1,17 @@
+[gene-expression]
+reference,working-directory/refdata-gex-GRCh38-2020-A/
+force-cells,9024
+check-library-compatibility,false
+
+[feature]
+reference,working-directory/final-analysis/feature_ref.csv
+
+[vdj]
+reference,working-directory/final-analysis/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,working-directory/bamtofastq/Donor1_healthy/demultiplexed_samples_0_1_HW7KMDSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,working-directory/fastqs/ab_fastq,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,working-directory/fastqs/tcr_fastq,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,working-directory/fastqs/bcr_fastq,VDJ-B
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor4_config.csv b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor4_config.csv
new file mode 100644
index 000000000..9fbd8d96b
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/Donor4_config.csv
@@ -0,0 +1,17 @@
+[gene-expression]
+reference,path/to/cellranger/prebuilt/human/refdata-gex-GRCh38-2020-A/
+force-cells,7032
+check-library-compatibility,false
+
+[feature]
+reference,/path/to/feature_ref.csv
+
+[vdj]
+reference,/path/to/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,/path/to/bamtofastq_outs_v1.4/Donor4_ALLpatient/PBMC_60k_10x_4tags_Rep1_step1_v7_0_1_HMW77DSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,/path/to/Ab-fastqs,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,/path/to/Ab-fastqs/TCR,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,/path/to/Ab-fastqs/BCR/,VDJ-B
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/README.md b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/README.md
new file mode 100644
index 000000000..2dce5701c
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/README.md
@@ -0,0 +1,209 @@
+# 60k Human PBMCs Multiplexed, 4 CMOs
+
+Peripheral blood mononuclear cells (PBMCs). Samples originate from two healthy donors (Donor 1 & 2), and from two patients diagnosed with Acute Lymphocytic Leukemia (Donor 3 & 4). Samples from donor 1,2, and 4 consist of peripheral blood mononuclear cells (PBMCs), while the sample from donor 3 consists of Bone Marrow Mononuclear Cells (BMMCs).
+Samples stained with TotalSeq-C antibodies both for cell surface protein (CSP) feature barcoding, but also for cell hashing, ie mimicing 3' cell multiplexing oligos (CMO). 
+Samples were pooled in a 1:1 ratio.
+
+Libraries were prepared following the Single Cell V(D)J Reagent Kits User Guide CG000424 (5' v2 HT) and sequenced on Illumina NovaSeq 6000.
+
+## Download original input data
+Data is available from 10x:
+[Demultiplexing 5’ Immune Profiling Libraries Pooled with Hashtags](https://www.10xgenomics.com/datasets/5-hashing-example-with-tabs-2-standard)
+
+```bash
+# Input Files
+curl -O https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5p_hashing_demux/5p_hashing_demux_gex_fastq.tar
+curl -O https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5p_hashing_demux/5p_hashing_demux_ab_fastq.tar
+curl -O https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5p_hashing_demux/5p_hashing_demux_tcr_fastq.tar
+curl -O https://cf.10xgenomics.com/samples/cell-vdj/7.0.0/5p_hashing_demux/5p_hashing_demux_bcr_fastq.tar
+curl -O https://cf.10xgenomics.com/samples/cell-vdj/7.0.0/5p_hashing_demux/5p_hashing_demux_cmo-set.csv
+curl -O https://cf.10xgenomics.com/samples/cell-vdj/7.0.0/5p_hashing_demux/5p_hashing_demux_config.csv
+```
+
+## Original `cellranger multi` configs
+Since this data consist of both multiplexed samples and immune profiling data, data must be processed as follows:
+
+1. Demultiplex by sample
+2. Convert BAM to FASTQ per sample
+3. Run cellranger for each sample
+
+See [this](https://www.10xgenomics.com/analysis-guides/demultiplexing-and-analyzing-5’-immune-profiling-libraries-pooled-with-hashtags) analysis guide.
+
+### Sample demultiplexing config (step 1)
+This config is to demultiplex by sample. This step requires GEX and CMO data.
+
+```bash
+[gene-expression]
+reference,/path/to/cellranger/prebuilt/human/refdata-gex-GRCh38-2020-A/
+cmo-set,/path/to/wrkdir/demultiplexing/5p_hashing_demux_cmo-set.csv
+
+[libraries]
+fastq_id,fastqs,feature_types
+PBMC-ALL_60k_universal_HashAB1-4_BL_4tags_Rep1_gex,Path/to/GEX/FASTQs,Gene Expression
+PBMC-ALL_60k_universal_HashAB1-4_BL_4tags_Rep1_ab,Path/to/AB/FASTQs,Multiplexing Capture
+
+[samples]
+sample_id,cmo_ids
+Donor1_healthy,Hash-tag1
+Donor2_healthy,Hash-tag2
+Donor3_ALLpatient,Hash-tag3
+Donor4_ALLpatient,Hash-tag4
+```
+
+### Convert BAM to FASTQ (step 2)
+For each sample output convert the GEX BAM file to FASTQ.
+This step requires the 10x provided bamtofastq binaries which is bundled with cellranger.
+Add `bamtofastq`to your `$PATH` like so:
+
+```bash
+# Command to change to the directory where the Cell Ranger executable file lives and put it in your $PATH:
+cd /path/to/cellranger-7.0.0/
+export PATH=${PWD}:$PATH
+
+# Command to put other tools bundled with Cell Ranger in your path:
+source /path/to/cellranger-7.0.0/sourceme.bash
+```
+
+Run `bamtofastq` per sample:
+```bash
+mkdir bamtofastq
+
+bamtofastq /path/to/wrkdir/demultiplexing/demultiplexed_samples/outs/per_sample_outs/Donor1_healthy/count/sample_alignments.bam /path/to/wrkdir/bamtofastq/Donor1_healthy
+bamtofastq /path/to/wrkdir/demultiplexing/demultiplexed_samples/outs/per_sample_outs/Donor2_healthy/count/sample_alignments.bam /path/to/wrkdir/bamtofastq/Donor2_healthy
+bamtofastq /path/to/wrkdir/demultiplexing/demultiplexed_samples/outs/per_sample_outs/Donor3_ALLpatient/count/sample_alignments.bam /path/to/wrkdir/bamtofastq/Donor3_ALLpatient
+bamtofastq /path/to/wrkdir/demultiplexing/demultiplexed_samples/outs/per_sample_outs/Donor4_ALLpatient/count/sample_alignments.bam /path/to/wrkdir/bamtofastq/Donor4_ALLpatient
+```
+
+Expected output:
+```bash
+$ ls /path/to/wrkdir/bamtofastq/Donor1_healthy
+
+demultiplexed_samples_0_1_HW7KMDSX3/ demultiplexed_samples_1_1_HW7WGDSX3/
+```
+
+Please note that the order of the libraries depends on the order that the libraries are listed in 5p_hashing_demux_config.csv (Step 1).
+The GEX library is listed before Multiplexing Capture, and therefore GEX data is found in `demultiplexed_samples_0_1_HW7KMDSX3/`.
+
+### Immune profiling per sample (step 3)
+This step must be run for each sample.
+
+```bash
+mkdir final-analysis
+```
+
+Below are listed configs for each sample.
+
+1. Donor
+```bash
+[gene-expression]
+reference,wrkdir/refdata-gex-GRCh38-2020-A/
+force-cells,11638
+check-library-compatibility,false
+
+[feature]
+reference,wrkdir/final-analysis/feature_ref.csv
+
+[vdj]
+reference,wrkdir/final-analysis/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,wrkdir/bamtofastq/Donor1_healthy/demultiplexed_samples_0_1_HW7KMDSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,wrkdir/fastqs/ab_fastq,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,wrkdir/fastqs/tcr_fastq,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,wrkdir/fastqs/bcr_fastq,VDJ-B
+```
+
+2. Donor 2
+```bash
+[gene-expression]
+reference,wrkdir/refdata-gex-GRCh38-2020-A/
+force-cells,8873
+check-library-compatibility,false
+
+[feature]
+reference,wrkdir/final-analysis/feature_ref.csv
+
+[vdj]
+reference,wrkdir/final-analysis/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,wrkdir/bamtofastq/Donor2_healthy/demultiplexed_samples_0_1_HW7KMDSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,wrkdir/fastqs/ab_fastq,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,wrkdir/fastqs/tcr_fastq,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,wrkdir/fastqs/bcr_fastq,VDJ-B
+```
+
+3. Donor 3
+```bash
+[gene-expression]
+reference,wrkdir/refdata-gex-GRCh38-2020-A/
+force-cells,9024
+check-library-compatibility,false
+
+[feature]
+reference,wrkdir/final-analysis/feature_ref.csv
+
+[vdj]
+reference,wrkdir/final-analysis/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,wrkdir/bamtofastq/Donor1_healthy/demultiplexed_samples_0_1_HW7KMDSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,wrkdir/fastqs/ab_fastq,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,wrkdir/fastqs/tcr_fastq,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,wrkdir/fastqs/bcr_fastq,VDJ-B
+```
+
+4. Donor 4
+```bash
+[gene-expression]
+reference,path/to/cellranger/prebuilt/human/refdata-gex-GRCh38-2020-A/
+force-cells,7032
+check-library-compatibility,false
+
+[feature]
+reference,/path/to/feature_ref.csv
+
+[vdj]
+reference,/path/to/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
+
+[libraries]
+fastq_id,fastqs,feature_types
+bamtofastq,/path/to/bamtofastq_outs_v1.4/Donor4_ALLpatient/PBMC_60k_10x_4tags_Rep1_step1_v7_0_1_HMW77DSX3,Gene Expression
+PBMC_60k_10x_4tags_Rep1_Ab,/path/to/Ab-fastqs,Antibody Capture
+PBMC_60k_10x_4tags_Rep1_TCR,/path/to/Ab-fastqs/TCR,VDJ-T
+PBMC_60k_10x_4tags_Rep1_BCR,/path/to/Ab-fastqs/BCR/,VDJ-B
+```
+
+Run cellranger multi:
+```bash
+cellranger multi --id=Donor1-final --csv=Donor1_config.csv
+cellranger multi --id=Donor2-final --csv=Donor2_config.csv
+cellranger multi --id=Donor3-final --csv=Donor3_config.csv
+cellranger multi --id=Donor4-final --csv=Donor4_config.csv
+```
+
+## Cell Multiplexing Data 
+
+The cell multiplexing libraries require more generous subsampling to yield sufficient reads for successful processing. 
+Test data use the first 3,500,000 lines of each of the lane 1 FASTQs.
+
+```bash
+#!/usr/bin/env bash
+
+ft_type=$1
+
+old="raw/fastq/${ft_type}/${ft_type}-PBMC-Control-1"
+for of in "${old}_"*.fastq.gz; do
+    new="raw_sub/fastqs/${ft_type}/subsampled_sc5p_PBMC_60k_${ft_type}"
+    nf=${of/$old/$new}
+    echo $of
+    echo $nf
+
+    zcat "$of" | \
+        head -n 3500000 | \
+        gzip - > $nf
+done
+```
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/cmo-set.csv b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/cmo-set.csv
new file mode 100644
index 000000000..eb38fa578
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/cmo-set.csv
@@ -0,0 +1,5 @@
+id,name,read,pattern,sequence,feature_type
+Hash-tag1,Hash-tag1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTCAACTCTTTAGCG,Multiplexing Capture
+Hash-tag2,Hash-tag2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGATGGCCTATTGGG,Multiplexing Capture
+Hash-tag3,Hash-tag3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTCCGCCTCTCTTTG,Multiplexing Capture
+Hash-tag4,Hash-tag4,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGTAAGTTCAGCGTA,Multiplexing Capture
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/AB/subsampled_sc5p_PBMC_60k_AB_Donor1_healthy_S1_L001_R1_001.fastq.gz b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/AB/subsampled_sc5p_PBMC_60k_AB_Donor1_healthy_S1_L001_R1_001.fastq.gz
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diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor1_healthy_S1_L001_R1_001.fastq.gz b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor1_healthy_S1_L001_R1_001.fastq.gz
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diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor1_healthy_S1_L001_R2_001.fastq.gz b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor1_healthy_S1_L001_R2_001.fastq.gz
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diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor2_healthy_S1_L001_R1_001.fastq.gz b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor2_healthy_S1_L001_R1_001.fastq.gz
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diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor2_healthy_S1_L001_R2_001.fastq.gz b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor2_healthy_S1_L001_R2_001.fastq.gz
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Binary files /dev/null and b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/GEX/subsampled_sc5p_PBMC_60k_GEX_Donor2_healthy_S1_L001_R2_001.fastq.gz differ
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/TCR/subsampled_sc5p_PBMC_60k_TCR_S1_L001_R1_001.fastq.gz b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/TCR/subsampled_sc5p_PBMC_60k_TCR_S1_L001_R1_001.fastq.gz
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diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/TCR/subsampled_sc5p_PBMC_60k_TCR_S1_L001_R2_001.fastq.gz b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/TCR/subsampled_sc5p_PBMC_60k_TCR_S1_L001_R2_001.fastq.gz
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Binary files /dev/null and b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/fastqs/TCR/subsampled_sc5p_PBMC_60k_TCR_S1_L001_R2_001.fastq.gz differ
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/feature-ref.csv b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/feature-ref.csv
new file mode 100644
index 000000000..1ac99c2f1
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/feature-ref.csv
@@ -0,0 +1,138 @@
+id,name,read,pattern,sequence,feature_type
+CD86,anti-human_CD86,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTCTTTGTCAGTGCA,Antibody Capture
+CD274,anti-human_CD274_B7-H1_PD-L1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTTGTCCGACAATAC,Antibody Capture
+CD270,anti-human_CD270_HVEM_TR2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGATAGAAACAGACC,Antibody Capture
+CD155,anti-human_CD155_PVR,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ATCACATCGTTGCCA,Antibody Capture
+CD112,anti-human_CD112_Nectin-2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AACCTTCCGTCTAAG,Antibody Capture
+CD47,anti-human_CD47,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCATTCTGTCACCTA,Antibody Capture
+CD48,anti-human_CD48,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTACGACGTAGAAGA,Antibody Capture
+CD40,anti-human_CD40,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTCAGATGGAGTATG,Antibody Capture
+CD154,anti-human_CD154,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCTAGATAGATGCAA,Antibody Capture
+CD52,anti-human_CD52,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTTTGTACGAGCAAA,Antibody Capture
+CD3,anti-human_CD3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTCATTGTAACTCCT,Antibody Capture
+CD8,anti-human_CD8,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCGCAACTTGATGAT,Antibody Capture
+CD56,anti-human_CD56,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCTTTCCTGATAGG,Antibody Capture
+CD19,anti-human_CD19,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTGGGCAATTACTCG,Antibody Capture
+CD33,anti-human_CD33,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TAACTCAGGGCCTAT,Antibody Capture
+CD11c,anti-human_CD11c,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TACGCCTATAACTTG,Antibody Capture
+HLA-A_B_C,anti-human_HLA-A_B_C,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TATGCGAGGCTTATC,Antibody Capture
+CD45RA,anti-human_CD45RA,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCAATCCTTCCGCTT,Antibody Capture
+CD123,anti-human_CD123,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTTCACTCTGTCAGG,Antibody Capture
+CD7,anti-human_CD7,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGGATTCCCGGACTT,Antibody Capture
+CD105,anti-human_CD105,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ATCGTCGAGAGCTAG,Antibody Capture
+CD49f,anti-human_mouse_CD49f,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTCCGAGGATGATCT,Antibody Capture
+CD194,anti-human_CD194_CCR4,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGCTTACCTGCACGA,Antibody Capture
+CD4,anti-human_CD4,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGTTCCCGCTCAACT,Antibody Capture
+CD44,anti-mouse_human_CD44,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGGCTTCAGGTCCTA,Antibody Capture
+CD14,anti-human_CD14,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCTCAGACCTCCGTA,Antibody Capture
+CD16,anti-human_CD16,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AAGTTCACTCTTTGC,Antibody Capture
+CD25,anti-human_CD25,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTTGTCCTGTACGCC,Antibody Capture
+CD45RO,anti-human_CD45RO,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTCCGAATCATGTTG,Antibody Capture
+CD279,anti-human_CD279,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACAGCGCCGTATTTA,Antibody Capture
+TIGIT,anti-human_TIGIT_VSTM3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTGCTTACCGCCAGA,Antibody Capture
+Mouse_IgG1_k_isotype_Ctrl,Mouse_IgG1_k_isotype_Ctrl,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCCGGACGACATTAA,Antibody Capture
+Mouse_IgG2a_k_isotype_Ctrl,Mouse_IgG2a_k_isotype_Ctrl,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTCCTACCTAAACTG,Antibody Capture
+Mouse_IgG2b_k_isotype_Ctrl,Mouse_IgG2b_k_isotype_Ctrl,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ATATGTATCACGCGA,Antibody Capture
+Rat_IgG2b_k_isotype_Ctrl,Rat_IgG2b_k_Isotype_Ctrl,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GATTCTTGACGACCT,Antibody Capture
+CD20,anti-human_CD20,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTCTGGGTCCCTAGA,Antibody Capture
+CD335,anti-human_CD335_NKp46,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACAATTTGAACAGCG,Antibody Capture
+CD31,anti-human_CD31,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACCTTTATGCCACGG,Antibody Capture
+CD146,anti-human_CD146,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCTTGGATAACATCA,Antibody Capture
+IgM,anti-human_IgM,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TAGCGAGCCCGTATA,Antibody Capture
+CD5,anti-human_CD5,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CATTAACGGGATGCC,Antibody Capture
+CD183,anti-human_CD183_CXCR3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCGATGGTAGATTAT,Antibody Capture
+CD195,anti-human_CD195_CCR5,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCAAAGTAAGAGCCA,Antibody Capture
+CD32,anti-human_CD32,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCTTCCGAATTACCG,Antibody Capture
+CD196,anti-human_CD196_CCR6,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GATCCCTTTGTCACT,Antibody Capture
+CD185,anti-human_CD185_CXCR5,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AATTCAACCGTCGCC,Antibody Capture
+CD103,anti-human_CD103_Integrin_aE,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GACCTCATTGTGAAT,Antibody Capture
+CD69,anti-human_CD69,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTCTCTTGGCTTAAA,Antibody Capture
+CD62L,anti-human_CD62L,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTCCCTGCAACTTGA,Antibody Capture
+CD161,anti-human_CD161,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTACGCAGTCCTTCT,Antibody Capture
+CD152,anti-human_CD152_CTLA-4,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ATGGTTCACGTAATC,Antibody Capture
+CD223,anti-human_CD223_LAG-3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CATTTGTCTGCCGGT,Antibody Capture
+KLRG1,anti-human_KLRG1_MAFA,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTTATTTCCTGCCCT,Antibody Capture
+CD27,anti-human_CD27,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCACTCCTGCATGTA,Antibody Capture
+CD107a,anti-human_CD107a_LAMP-1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CAGCCCACTGCAATA,Antibody Capture
+CD95,anti-human_CD95_Fas,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCAGCTCATTAGAGC,Antibody Capture
+CD134,anti-human_CD134_OX40,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AACCCACCGTTGTTA,Antibody Capture
+HLA-DR,anti-human_HLA-DR,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AATAGCGAGCAAGTA,Antibody Capture
+CD1c,anti-human_CD1c,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GAGCTACTTCACTCG,Antibody Capture
+CD11b,anti-human_CD11b,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GACAAGTGATCTGCA,Antibody Capture
+CD64,anti-human_CD64,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AAGTATGCCCTACGA,Antibody Capture
+CD141,anti-human_CD141_Thrombomodulin,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GGATAACCGCGCTTT,Antibody Capture
+CD1d,anti-human_CD1d,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCGAGTCGCTTATCA,Antibody Capture
+CD314,anti-human_CD314_NKG2D,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CGTGTTTGTTCCTCA,Antibody Capture
+CD35,anti-human_CD35,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACTTCCGTCGATCTT,Antibody Capture
+CD57,anti-human_CD57_Recombinant,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AACTCCCTATGGAGG,Antibody Capture
+CD272,anti-human_CD272_BTLA,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTTATTGGACTAAGG,Antibody Capture
+CD278,anti-human_mouse_rat_CD278_ICOS,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CGCGCACCCATTAAA,Antibody Capture
+CD58,anti-human_CD58_LFA-3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTTCCTATGGACGAC,Antibody Capture
+CD39,anti-human_CD39,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTACCTGGTATCCGT,Antibody Capture
+CX3CR1,anti-human_CX3CR1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGTATCGTCTCTGGG,Antibody Capture
+CD24,anti-human_CD24,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGATTCCTTCGTGTT,Antibody Capture
+CD21,anti-human_CD21,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AACCTAGTAGTTCGG,Antibody Capture
+CD11a,anti-human_CD11a,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TATATCCTTGTGAGC,Antibody Capture
+CD79b,anti-human_CD79b_Ig,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ATTCTTCAACCGAAG,Antibody Capture
+CD244,anti-human_CD244_2B4,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCGCTTGGATGGTAG,Antibody Capture
+CD169,anti-human_CD169_Sialoadhesin_Siglec-1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TACTCAGCGTGTTTG,Antibody Capture
+integrin_b7,anti-human_mouse_integrin_b7,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCTTGGATGTACCG,Antibody Capture
+CD268,anti-human_CD268_BAFF-R,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CGAAGTCGATCCGTA,Antibody Capture
+CD42b,anti-human_CD42b,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCTAGTACCGAAGT,Antibody Capture
+CD54,anti-human_CD54,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTGATAGACTTGAGT,Antibody Capture
+CD62P,anti-human_CD62P_P-Selectin,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCTTCCGTATCCCTT,Antibody Capture
+CD119,anti-human_CD119_IFN-y_R_a_chain,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGTGTATTCCCTTGT,Antibody Capture
+TCRa_b,anti-human_TCR_a_or_b,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CGTAACGTAGAGCGA,Antibody Capture
+Rat_IgG1_k_isotype_Ctrl,Rat_IgG1_k_isotype_Ctrl,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ATCAGATGCCCTCAT,Antibody Capture
+Rat_IgG2a_k_isotype_Ctrl,Rat_IgG2a_k_Isotype_Ctrl,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AAGTCAGGTTCGTTT,Antibody Capture
+Armenian_Hamster_IgG_Isotype_Ctrl,Armenian_Hamster_IgG_Isotype_Ctrl,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCTGTCATTAAGACT,Antibody Capture
+CD122,anti-human_CD122_IL-2Rb,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCATTTCCTCCGATT,Antibody Capture
+CD267,anti-human_CD267_TACI,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGTGATGGAGCGAAC,Antibody Capture
+FceRIa,anti-human_FceRIa,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTCGTTTCCGTATCG,Antibody Capture
+CD41,anti-human_CD41,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACGTTGTGGCCTTGT,Antibody Capture
+CD137,anti-human_CD137_4-1BB,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CAGTAAGTTCGGGAC,Antibody Capture
+CD163,anti-human_CD163,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCTTCTCCTTCCTTA,Antibody Capture
+CD83,anti-human_CD83,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCACTCATTTCCGGT,Antibody Capture
+CD124,anti-human_CD124_IL-4R,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCGTCCTGATAGATG,Antibody Capture
+CD13,anti-human_CD13,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTTCAACGCCCTTTC,Antibody Capture
+CD2,anti-human_CD2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TACGATTTGTCAGGG,Antibody Capture
+CD226,anti-human_CD226_DNAM-1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCTCAGTGTTTGTGG,Antibody Capture
+CD29,anti-human_CD29,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTATTCCCTCAGTCA,Antibody Capture
+CD303,anti-human_CD303_BDCA-2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GAGATGTCCGAATTT,Antibody Capture
+CD49b,anti-human_CD49b,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCTTTCTTCAGTATG,Antibody Capture
+CD81,anti-human_CD81_TAPA-1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTATCCTTCCTTGGC,Antibody Capture
+IgD,anti-human_IgD,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CAGTCTCCGTAGAGT,Antibody Capture
+CD18,anti-human_CD18,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TATTGGGACACTTCT,Antibody Capture
+CD28,anti-human_CD28,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGAGAACGACCCTAA,Antibody Capture
+CD38,anti-human_CD38,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGTACCCGCTTGTGA,Antibody Capture
+CD127,anti-human_CD127_IL-7Ra,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GTGTGTTGTCCTATG,Antibody Capture
+CD45,anti-human_CD45,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGCAATTACCCGGAT,Antibody Capture
+CD22,anti-human_CD22,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GGGTTGTTGTCTTTG,Antibody Capture
+CD71,anti-human_CD71,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCGTGTTCCTCATTA,Antibody Capture
+CD26,anti-human_CD26,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GGTGGCTAGATAATG,Antibody Capture
+CD36,anti-human_CD36,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TTCTTTGCCTTGCCA,Antibody Capture
+CD158,anti-human_CD158_KIR2DL1_S1_S3_S5,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TATCAACCAACGCTT,Antibody Capture
+CD49a,anti-human_CD49a,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACTGATGGACTCAGA,Antibody Capture
+CD49d,anti-human_CD49d,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCATTCAACTTCCGG,Antibody Capture
+CD73,anti-human_CD73_Ecto-5-nucleotidase,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CAGTTCCTCAGTTCG,Antibody Capture
+TCRV_7-2,anti-human_TCR_V_7-2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TACGAGCAGTATTCA,Antibody Capture
+TCRV_2,anti-human_TCR_V_2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCAGTCAGATGGTAT,Antibody Capture
+LOX-1,anti-human_LOX-1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACCCTTTACCGAATA,Antibody Capture
+CD158b,anti-human_CD158b_KIR2DL2_L3_NKAT2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GACCCGTAGTTTGAT,Antibody Capture
+CD158e1,anti-human_CD158e1_KIR3DL1_NKB1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GGACGCTTTCCTTGA,Antibody Capture
+CD319,anti-human_CD319_CRACC,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGTATGCCATGTCTT,Antibody Capture
+CD99,anti-human_CD99,R2,^NNNNNNNNNN(BC)NNNNNNNNN,ACCCGTCCCTAAGAA,Antibody Capture
+CLEC12A,anti-human_CLEC12A,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CATTAGAGTCTGCCA,Antibody Capture
+CD352,anti-human_CD352_NTB-A,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGTTTCCACTCAGGC,Antibody Capture
+CD94,anti-human_CD94,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTTTCCGGTCCTACA,Antibody Capture
+Ig_light_chain_k,anti-human_Ig_light_chain_k,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AGCTCAGCCAGTATG,Antibody Capture
+CD85j,anti-human_CD85j_ILT2,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CCTTGTGAGGCTATG,Antibody Capture
+CD23,anti-human_CD23,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCTGTATAACCGTCT,Antibody Capture
+Ig_light_chain_g,anti-human_Ig_light_chain_gamma,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CAGCCAGTAAGTCAC,Antibody Capture
+CD328,anti-human_CD328_Siglec-7,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTTAGCATTTCACTG,Antibody Capture
+GPR56,anti-human_GPR56,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCCTAGTTTCCGTTT,Antibody Capture
+HLA-E,anti-human_HLA-E,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GAGTCGAGAAATCAT,Antibody Capture
+CD82,anti-human_CD82,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCCACTTCCGCTTT,Antibody Capture
+CD101,anti-human_CD101_BB27,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTACTTCCCTGTCAA,Antibody Capture
+CD88,anti-human_CD88_C5aR,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCCGCATGAGAAACA,Antibody Capture
+CD224,anti-human_CD224,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTGATGAGATGTCAG,Antibody Capture
diff --git a/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/sample_demultiplexing_config.csv b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/sample_demultiplexing_config.csv
new file mode 100644
index 000000000..cb622a4fa
--- /dev/null
+++ b/data/genomics/homo_sapiens/10xgenomics/cellranger/60k_pbmc_cmo_tcr/sample_demultiplexing_config.csv
@@ -0,0 +1,15 @@
+[gene-expression]
+reference,/path/to/cellranger/prebuilt/human/refdata-gex-GRCh38-2020-A/
+cmo-set,/path/to/working-directory/demultiplexing/5p_hashing_demux_cmo-set.csv
+
+[libraries]
+fastq_id,fastqs,feature_types
+PBMC-ALL_60k_universal_HashAB1-4_BL_4tags_Rep1_gex,Path/to/GEX/FASTQs,Gene Expression
+PBMC-ALL_60k_universal_HashAB1-4_BL_4tags_Rep1_ab,Path/to/AB/FASTQs,Multiplexing Capture
+
+[samples]
+sample_id,cmo_ids
+Donor1_healthy,Hash-tag1
+Donor2_healthy,Hash-tag2
+Donor3_ALLpatient,Hash-tag3
+Donor4_ALLpatient,Hash-tag4