The following softwares have been installed in January-February 2022

• parsnp version: 1.5.6

  Description: Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours
  Based on conda package.

  URL: https://github.com/marbl/parsnp
  

  Command to load its environment: module load bioinfo/parsnp/1.5.6

• MitoZ: 2.3

  Description: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
  Based on a singularity container

  URL: https://github.com/linzhi2013/MitoZ

  Command to load its environment: module load bioinfo/MitoZ/2.3

• ipyrad version: 0.9.82

  Description: an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies

  URL: https://github.com/dereneaton/ipyrad

  Command to load its environment: module load bioinfo/ipyrad/0.9.82

• STACKS version: 2.60

  Description: Stacks is a software pipeline for building loci from short-read sequences

  URL: https://catchenlab.life.illinois.edu/stacks/

  Command to load its environment: module load bioinfo/stacks/2.60

• syri version: 1.5.1

  Description: SyRI is a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions.

  URL: https://schneebergerlab.github.io/syri

  Command to load its environment: module load bioinfo/syri/1.5.1

• seqkit version: 2.1.0

  Description: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

  URL: https://bioinf.shenwei.me/seqkit/
  

  Command to load its environment: module load bioinfo/seqkit/2.1.0

• fastqsplitter version: 1.2.0

  Description: A simple application to split FASTQ files.

  URL: https://pypi.org/project/fastqsplitter/

  Command to load its environment: module load bioinfo/fastqsplitter/1.2.0

• PICRUSt version: 1.1.4

  Description: Logiciel Python pour faire de la prédiciton en métagénomique à partir de données 16S

  URL: https://picrust.github.io/picrust/install.html

  Command to load its environment: module load bioinfo/picrust/1.1.4

• bwa-mem2 version: 2.2.1

  Description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.

  URL: https://github.com/bwa-mem2/bwa-mem2

  Command to load its environment: module load bioinfo/bwamem2/2.2.1

• gmap version: 2021-12-17

  Description: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program

  URL: http://research-pub.gene.com/gmap/

  Command to load its environment: module load bioinfo/gmap/2021-12-17

• uvaia version: 1.0

  Description: a program for pairwise reference-based alignment, and subsequent search against an aligned database.

  URL: https://github.com/quadram-institute-bioscience/uvaia
  

  Command to load its environment: module load bioinfo/uvaia/1.0

• iqtree2 version: 2.2.0-beta

  Description: Efficient and versatile phylogenomic software by maximum likelihood

  URL: http://www.iqtree.org/doc/Quickstart#installation
  

  Command to load its environment: module load bioinfo/iqtree/2.2.0-beta

• MaSurca version: 4.0.8

  Description: Short reads assembly

  URL: https://github.com/alekseyzimin/masurca/
  

  Command to load its environment: module load bioinfo/MaSuRCA/4.0.8

• nextclade version: 1.10.3

  Description: Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

  URL: https://github.com/nextstrain/nextclade
  

  Command to load its environment: module load bioinfo/nextclade/1.10.3