**[[https://meso-centres-lyon.pages.in2p3.fr/psmn-rtd/index.html|New Documentation (Debian 11 / Slurm)]]** See also our [[news:blog|Fil des news]] for up-to-date informations ====== Logiciels Bioinformatiques ====== * Alignment * [[documentation:tools:software:blat|BLAT]] * [[documentation:tools:software:blast|NCBI BLAST2 / BLAST+]] * [[documentation:tools:software:bowtie|Bowtie]] * [[documentation:tools:software:bwakit|BWA]] (Bwakit) * [[documentation:tools:software:clustalomega|ClustalOmega]] * [[documentation:tools:software:exonerate|Exonerate]] * [[documentation:tools:software:gblocks|Gblocks]] * [[documentation:tools:software:gmap-gsnap|GMAP/GSNAP]] * [[documentation:tools:software:mafft|MAFFT]] * [[documentation:tools:software:prank|Prank]] * [[documentation:tools:software:seaview|SeaView]] * [[documentation:tools:software:snap|SNAP]] * [[documentation:tools:software:star|STAR]] * [[documentation:tools:software:tcoffee|T-Coffee]] * [[documentation:tools:software:hmmer|HMMER /HMMER2]] * Genome Assembly * [[documentation:tools:software:pbsuite|PBSuite]] * [[documentation:tools:software:spades|SPAdes]] * [[documentation:tools:software:velvet|Velvet]] * Transcriptomes Assembly * [[documentation:tools:software:cufflinks|Cufflinks]] * [[documentation:tools:software:hisat|HISAT]] * [[documentation:tools:software:kallisto|kallisto]] * [[documentation:tools:software:kissplice|KisSplice]] * [[documentation:tools:software:star|STAR]] * [[documentation:tools:software:stringtie|StringTie]] * [[documentation:tools:software:tophat|TopHat]] * MaLTA [[http://alan.cs.gsu.edu/NGS/?q=malta|.]] * //de novo// assembly * |aTRAM * apytram * Bridger * [[documentation:tools:software:canu|Canu]] * Celera-WGS * [[documentation:tools:software:corset|Corset]] * [[documentation:tools:software:mira|MIRA]] * Oases * [[documentation:tools:software:stringtie|StringTie]] * [[documentation:tools:software:trinity|Trinity]] * [[documentation:tools:software:velvet|Velvet]] * Genome/Transcriptome Annotation * [[documentation:tools:software:augustus|Augustus]] * [[documentation:tools:software:braker|Braker]] * [[documentation:tools:software:genemark|GeneMark ES/ET]] * [[documentation:tools:software:transdecoder|TransDecoder]] * Sequences clustering * SiLiX * Estimate RNA-seq Abundance * [[documentation:tools:software:cufflinks|Cufflinks]] * [[documentation:tools:software:gfold|GFOLD]] * [[documentation:tools:software:htseq|HTSeq]] * [[documentation:tools:software:kallisto|kallisto]] * [[documentation:tools:software:rsem|RSEM]] * [[documentation:tools:software:salmon|Salmon]] * [[documentation:tools:software:stringtie|StringTie]] * SNP * [[documentation:tools:software:bcftools|BCFtools]] * [[documentation:tools:software:breseq|breseq]] * [[documentation:tools:software:discosnp|DiscoSNP]] * [[documentation:tools:software:gatk|GATK]] * [[documentation:tools:software:kissplice|KisSplice]] * [[documentation:tools:software:snpeff|SnpEff]] * SNPScanner * Phylogeny * [[documentation:tools:software:fasttree|FastTree]] * [[documentation:tools:software:gubbins|Gubbins]] * [[documentation:tools:software:hyphy|HyPhy]] * [[documentation:tools:software:mrbayes|MRbayes]] * PHYLDOG * [[documentation:tools:software:phyml|PhyML]] * [[documentation:tools:software:raxml|RAxML]] * [[documentation:tools:software:seaview|SeaView]] * Guidance & Guidance2 * ChIP-seq Analysis * [[documentation:tools:software:drompa|DROMPA]] * [[documentation:tools:software:macs|MACS/MACS2]] * [[documentation:tools:software:music|MUSIC]] * [[documentation:tools:software:odin|ODIN]] * Nucleosomes Mapping * NucleoMiner * Handle NGS Data * [[documentation:tools:software:bamtools|BamTools]] * [[documentation:tools:software:bedtools|BEDTools]] * [[documentation:tools:software:fastq-tools|fastq-tools]] * [[documentation:tools:software:fastx-toolkit|FASTX-Toolkit]] * [[documentation:tools:software:htseq|HTSeq]] * [[documentation:tools:software:htslib|HTSlib]]/[[documentation:tools:software:bcftools|bcftools]]/[[documentation:tools:software:samtools|SAMtools]] * [[documentation:tools:software:picard|Picard]] * [[documentation:tools:software:sratoolkit|SRAToolkit]] * [[documentation:tools:software:tablemaker|tablemaker]] * [[documentation:tools:software:jellyfish|Jellyfish]] * Homer * NGS data visualization * [[documentation:tools:software:pybigwig|pyBigWig]] * [[documentation:tools:software:ucsc|UCSC]] * Trim rna-seq reads * [[documentation:tools:software:prinseq-lite|prinseq-lite]] * [[documentation:tools:software:trimmomatic|Trimmomatic]] * Libraries /Languages * [[documentation:tools:software:biopython|Biopython]] * [[documentation:tools:software:seqan|SeqAn]] * [[documentation:tools:langages:perl5|Perl5]] BioPerl * [[documentation:tools:software:r|R]] * NGS suites * [[documentation:tools:software:meme|MEME Suite]] * [[documentation:tools:software:novocraft|NovoCraft]] * [[documentation:tools:software:trinotate|Trinotate]] * [[documentation:tools:software:ucsc|UCSC]] * Quality Control NGS Data * [[documentation:tools:software:fastqc|FastQC]] * [[documentation:tools:software:rnaseqc|RNAseq-QC]] * [[documentation:tools:software:rseqc|RSeQC]] * [[documentation:tools:software:quast|Quast]] * Bisulfite mapping methylation call * [[documentation:tools:software:bismark|Bismark]] * Clustering * [[documentation:tools:software:cafs|CAFS]] * Detection of reconbination * [[documentation:tools:software:clonalframeml|ClonalFrameML]] * DNA methylation * [[documentation:tools:software:dmap|DMAP]] * Tools for Molecular Biology * [[documentation:tools:software:emboss|EMBOSS Suite]] * PCR Primers * [[documentation:tools:software:primer3|Primer3]] * NMR * Spinevolution * DNase-seq Analysis * [[documentation:tools:software:pydnase|pyDNase]] * Predict RNA secondary strucures * [[documentation:tools:software:viennarna|ViennaRNA]] \\ ------------------------------------------------------------------- \\ Vous pouvez visiter le site [[https://bio.tools/|BioTools d'Elixir]] qui a pour but de recenser et de classer les outils bioinformatiques.