Vous trouverez dans cette rubrique une liste des logiciels de BIO installés sur CALI et les informations nécessaires pour leur utilisation sous slurm.
Notez que l'environnement utilisateur est géré à travers des modules : ces modules donnent accès à tel ou tel logiciel, dans des versions spécifiques. L'utilisation d'un logiciel nécessite donc en général le chargement d'un module associé. Lire la page de présentation des modules
| page | desc |
|---|---|
| bcl2fastq | bcl2fastq Logiciel de transformation de format des données de séquençage génétique. * Versions installées : * 2.17.1.14 Utilisation Sélection de la version Pour sélectionner la version voulue : utiliser les modules bcl2fastq a été placé dans l'ensemble |
| beagle | Beagle
Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
* Site web : |
| bedtools | Bedtools Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. |
| bio | Bio++ Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is fully Object Oriented and is designed to be both easy to use and computer efficient. * Site web : |
| blat | blat BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates. |
| bowtie-2 | Bowtie-2
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
* Site web : |
| bowtie | Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner geared
toward quickly aligning large sets of short DNA sequences (reads) to
large genomes.
* Site web : |
| bwa | BWA
BWA is a software package for mapping DNA sequences against a large reference
genome, such as the human genome.
* Site web : |
| cufflinks | Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. |
| cutadapt | cutadapt cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs. * Site web : |
| deeptools | deeptools
“tools for exploring deep sequencing data” : deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
* Site web : |
| fastq-tools | fastq-tools
Small utilities for working with fastq sequence files.
* Site web : |
| fastqc | fastqc
FastQC is an application which takes a FastQ file and runs a series
of tests on it to generate a comprehensive QC report
* Site web : |
| fastx | LOGICIEL
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
* Site web : |
| gatk | gatk The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
| gblocks | LOGICIEL
Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.
* Site web : |
| gs3 | GS3 GS3 is a program that estimates fixed and random effects, breeding values and SNP effects for genomic selection. It includes normal, mixture, or double exponential distributions for SNP effects, i.e. GBLUP, the so-called BayesCPi, and the Bayesian Lasso. It allows estimation of the variances and effects of SNPs, polygenic and environmental effects, and also the inclusion of heterogeneous variances as for the analysis of DYD's. |
| htseq | HTSeq
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
* Site web : |
| igv | IGV The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. |
| mafft | MAFFT
* Site web : |
| mapsplice | MapSplice
MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.
* Site web : |
| mira | MIRA MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 16 years to get assembly jobs done efficiently - and especially accurately. That is, without actually putting too much manual work into finishing the assembly. |
| picard | Picard A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. Picard is implemented using the HTSJDK Java library HTSJDK, supporting accessing of common file formats, such as SAM and VCF, used for high-throughput sequencing data. |
| samtools | Samtools Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate software suites : Samtools, BCFtools and the HTSlib library. * Samtools : Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format |
| tophat | TopHat TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. |
| vcftools | vcftools VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |