diff --git a/docs/mag_workflow.dio b/docs/mag_workflow.dio index 4ec7c270..0737f57e 100644 --- a/docs/mag_workflow.dio +++ b/docs/mag_workflow.dio @@ -1,15 +1,15 @@ - + - + - + - + @@ -20,7 +20,7 @@ - + @@ -28,13 +28,13 @@ - + - + @@ -42,12 +42,12 @@ - + - + @@ -56,7 +56,7 @@ - + @@ -64,12 +64,12 @@ - + - + @@ -77,24 +77,24 @@ - + - + - + - + - + @@ -127,66 +127,66 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + diff --git a/docs/mag_workflow.svg b/docs/mag_workflow.svg index 923c3548..6e550451 100644 --- a/docs/mag_workflow.svg +++ b/docs/mag_workflow.svg @@ -1 +1 @@ -
Metagenome assembly
Metagenome assembly
Scaftigs, GFA, Report
Scaftigs, GFA, Report
Binning
Binning
MAGs, N50
MAGs, N50
Quality check 
Quality check 
High and medium quality MAGs
High and medium qua...
Metagenomics shut-gut reads
Metagenomics shut-gut reads
Quality control
Quality control
IDBA-UD
MEGAHIT
MetaSPAdes
OPERA-MS, plass
IDBA-UD...
MetaBAT2, MaxBin2, CONCOCT
GraphBin, DASTools
VAMB
MetaBAT2, MaxBin2, CONC...
OAs1 or sickle or fastp
BWA or Bowtie2
OAs1 or sickle or fastp...
seqtk
metapi::assembler
seqtk...
seqtk
metapi::binner
seqtk...
Dereplicate
Dereplicate
GTDBtk
dRep or galah
GTDBtk...
CheckM
GUNC
CheckM...
GTDBtk taxonomic assignment
GTDBtk taxonomic a...
QC-reads and QC-report
QC-reads and QC-re...
Software supported
Software supported
Process and results
Process and results
Annotation
Annotation
Reads layout: PE or SE
Reads format: FASTQ or SRA
Reads layout: PE or SE...
Trimming: choose only one from OAs1, sickle fastp
Rmhost: choose only one from BWA or Bowtie2,
Trimming and rmhost are optional
Trimming: choose only one from...
MGI/Illunima Sequencer or SRATools
MGI/Illunima Sequenc...
seqkit
metapi::qcer
seqkit...
Assembly mode(all support):
1. single assembly with IDBA-UD, MEGAHIT or MetaSPAdes
2. co-assembly with MEGAHIT
3. short-long hybrid assembly with OPERA-MS
4. protein assembly with plass
Assembly mode(all support):...
Binning mode(all support):
1. single-sample assembly and binning
2. multi-sample co-assemlby and binning
3. single sample assembly and multi-sample binning
Binning mode(all support):...
Choose representative MAG on species or strain level
Choose representative MAG on...
Compute completeness, contamination and others, based on MIMAG standard to choose high and medium quality MAG
Compute completeness, contami...
MAGs catalogue
MAGs catalogue
MAG workflow
MAG workflow
metapi::checkmer
metapi::checkmer
Viewer does not support full SVG 1.1
\ No newline at end of file +
Metagenome assembly
Metagenome assembly
Scaftigs, GFA, Report
Scaftigs, GFA, Report
Binning
Binning
MAGs, N50
MAGs, N50
Quality check 
Quality check 
High and medium quality MAGs
High and medium qua...
Metagenomics shot-gun reads
Metagenomics shot-gun reads
Quality control
Quality control
IDBA-UD
MEGAHIT
MetaSPAdes
OPERA-MS, plass
IDBA-UD...
MetaBAT2, MaxBin2, CONCOCT
GraphBin, DASTools
VAMB
MetaBAT2, MaxBin2, CONC...
OAs1 or sickle or fastp
BWA or Bowtie2
OAs1 or sickle or fastp...
seqtk
metapi::assembler
seqtk...
seqtk
metapi::binner
seqtk...
Dereplicate
Dereplicate
GTDBtk
dRep or galah
GTDBtk...
CheckM
GUNC
CheckM...
GTDBtk taxonomic assignment
GTDBtk taxonomic a...
QC-reads and QC-report
QC-reads and QC-re...
Software supported
Software supported
Process and results
Process and results
Annotation
Annotation
Reads layout: PE or SE
Reads format: FASTQ or SRA
Reads layout: PE or SE...
Trimming: choose only one from OAs1, sickle fastp
Rmhost: choose only one from BWA or Bowtie2,
Trimming and rmhost are optional
Trimming: choose only one from...
MGI/Illunima Sequencer or SRATools
MGI/Illunima Sequenc...
seqkit
metapi::qcer
seqkit...
Assembly mode(all support):
1. single assembly with IDBA-UD, MEGAHIT or MetaSPAdes
2. co-assembly with MEGAHIT
3. short-long hybrid assembly with OPERA-MS
4. protein assembly with plass
Assembly mode(all support):...
Binning mode(all support):
1. single-sample assembly and binning
2. multi-sample co-assemlby and binning
3. single sample assembly and multi-sample binning
Binning mode(all support):...
Choose representative MAG on species or strain level
Choose representative MAG on...
Compute completeness, contamination and others, based on MIMAG standard to choose high and medium quality MAG
Compute completeness, contami...
MAGs catalogue
MAGs catalogue
MAG workflow
MAG workflow
metapi::checkmer
metapi::checkmer
Viewer does not support full SVG 1.1
\ No newline at end of file