4.0.2

Version 4.0.2 (Sep 22nd, 2022)

New features

• [MetaPhlAn] The new --subsampling parameter allows reads' subsampling on the flight
• [MetaPhlAn] The new --subsampling_seed parameter enables a deterministic or randomized subsampling of the reads
• [MetaPhlAn] The new --gtdb_profiles of the merge_metaphlan_profiles.tsv allows the merge of GTDB-based MetaPhlAn profiles
• [StrainPhlAn] The new --breadth_thres parameter allows StrainPhlAn to filter the consensus markers sequences after the execution of sample2markers.py
• [StrainPhlAn] Interactive selection of the available SGBs when the clade is specified at the species level
• [StrainPhlAn] The new --non_interactive parameter disables user interaction when running StrainPhlAn
• [StrainPhlAn] The new --abs_n_markers_thres and --abs_n_samples_thres parameters enables the specification of the samples/markers filtering thresholds in absolute numbers
• [StrainPhlAn] The new --treeshrink parameter enables StrainPhlAn to run TreeShrink for outlier removal in the tree
• [StrainPhlAn] Addition of the VallesColomerM_2022_Jan21_thresholds.tsv for compatibility with the mpa_vJan21 database
• [StrainPhlAn] The new --clades parameter enables sample2markers.py to restrict the reconstruction of markers to the specified clades

Changed features

• [StrainPhlAn] The -c parameter of the extract_markers.py script now allows the specification of multiple clades
• [StrainPhlAn] The --print_clades_only parameter now produces an output print_clades_only.tsv report
• [StrainPhlAn] Compatibility with clade markers compressed in bz2 format
• [StrainPhlAn] The strain_transmission.py script now uses by the default the VallesColomerM_2022_Jan21_thresholds.tsv thresholds

Fixes

• [MetaPhlAn] metaphlan2krona.py and hclust2 have been added to the bioconda recipe