bioinfo@ird.fr

Installation de logiciels en janvier-Février 2022

Les logiciels suivants ont été installés en janvier-Février 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

    Commande pour charger son environnement: 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

    Commande pour charger son environnement: 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

    Commande pour charger son environnement: 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/

    Commande pour charger son environement: 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

    Commande pour charger son environnement: 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/

    Commande pour charger son environnement: 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/

    Commande pour charger son environnement: 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

    Commande pour charger son environnement: 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

    Commande pour charger son environnement: 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/

    Commande pour charger son environnement: 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

    Commande pour charger son environnement: 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

    Commande pour charger son environnement: module load bioinfo/iqtree/2.2.0-beta

  • MaSurca version: 4.0.8

    Description: Short reads assembly

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

    Commande pour charger son environnement: 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

    Commande pour charger son environnement: module load bioinfo/nextclade/1.10.3