4.1.0

Version 4.1.0 (Feb 20th, 2024)

Database updates

• We just released the new vJun23 database
  • Addition of ~45k reference genomes from NCBI
  • Addition of ~50k MAGs from ocean, ~40k MAGs from soil, ~30k MAGs from domestic animals and non-human primates, ~4k MAGs from giant turtles, ~7.5k MAGs from skin microbiome, ~20k MAGs from dental plaque, ~15k MAGs from Asian populations, ~2.7k MAGs from ancient and modern Bolivians and other small datasets from diverse sources
  • Expansion of the markers database with 36,822 SGBs (6,272 more SGBs than in vOct22)
• Inclusion of the new Viral Sequence Clusters (VSCs) database
  • Containing 3,944 VSCs clustered into 1,345 Viral Sequence Groups (VSGs).
  • Including a total of 45,872 representative VSGs sequences.
  • Each cluster/group is labeled as known (kVSG) or unknown (uVSG) depending on the presence of at least a viral RefSeq reference genome within the cluster/group.

New features

• [MetaPhlAn] The new --profile_vsc parameter (together with --vsc_out and --vsc_breadth) enables the profiling of viral sequence clusters.
• [MetaPhlAn] The --subsampling now subsamples the FASTQ files and not the mapping results
• [MetaPhlAn] The new --mapping_subsampling parameter enables the previous mapping subsampling behaviour
• [MetaPhlAn] The new --subsampling_output parameter enables to save the subsampled FASTQ file
• [MetaPhlAn] The new create_toy_database.py script enables the custom filtering of the MetaPhlAn databases

Changed features

• [MetaPhlAn] The average read length is included in the output header with the -t rel_ab_w_read_stats parameter
• [StrainPhlAn] Quasi-markers behaviour in line with that of MetaPhlAn
• [StrainPhlAn] sample2markers.py output is now in JSON format
• [StrainPhlAn] Simplified sample and marker filtering parameters, integrated with primary/secondary samples
• [StrainPhlAn] Faster inference of small and medium phylogenies
• [StrainPhlAn] Faster execution of the parameter –-print_clades_only