forge.ird.fr / phim 16 Repositories
Dépôt de code de l'unité [Plant Health Institute of Montpellier](https://umr-phim.cirad.fr/) Référents: [COMTE Aurore](mailto:aurore.comte@ird.fr), [DEREEPER Alexis](mailtoalexis.dereeper@ird.fr), [CUNNAC Sébastien](mailto:sebastien.cunnac@ird.fr), [RAVEL Sébastien](mailto:sebastien.ravel@cirad.fr)
phim/xplain/xplain_grist_dbs
This is a place were sits everything that is needed to implement the xplain girst instance that gather our databases (images, widgets, etc...) appart of course from the girst files themselves that need to remain private.
Last synced at: 7 months ago - Stars: 0 - Forks: 0
phim/cunnac/r_cibig_2024
Material used to teach the R module at the 2024 session of the International Certificate in Bioinformatics and Genomics (CIBiG).
Last synced at: 7 months ago - Stars: 0 - Forks: 0
phim/cunnac/genomicsr
A, still very experimental, R package that acts as a storage location for functions and interfaces in connection with genomics (genomes, transcriptomes, annotation, phylogenomics, ...)
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
phim/sravel/snakecdysis
Are you looking for a simplified installation process for your Snakemake workflows, including the various Python packages and the multitude of tools used by your pipelines? Would you like to simplify the use of your workflows with user-friendly commands and subcommands that even non-bioinformatician users can easy use? Look no further - Snakecdysis is the solution for you!
Last synced at: 7 months ago - Stars: 2 - Forks: 0
phim/sravel/PodiumASM
Long-read sequencing is a highly accurate approach that can be used to challenging genomes, such as those containing stretches of highly repetitive elements and lot of structural variant. Long read sequencing can also be used to generate de novo assembly and genome finishing applications Lot of tools are used to make genome assembly with long reads every day and sometimes you don't know wich Assembler tool is the best for your organism. PodiumASM is here for you ! PodiumASM is is an open-source, scalable, modulable and traceable snakemake pipeline, able to compare multiple long read assemblies obtained from multiple assemblers tools. The workflow PodiumASM can help you to choose the best assemblies among all possibilities.
Last synced at: 7 months ago - Stars: 1 - Forks: 0
phim/sravel/RattleSNP
snakemake workflow for mappind single/paired datas
Last synced at: 7 months ago - Stars: 2 - Forks: 0
phim/sravel/DNAnnot
This pipeline is an automatic structural annotation workflows written in snakemake. The annotation is based on two tools which uses RNA-Seq and/or protein homology information for predict coding sequence. One of this tools is BRAKER which use GeneMark-EX and AUGUSTUS. And the other tool is AUGUSTUS alone for improve annotation of small coding sequences with few or no intron. Before the annotation, the repeat element of genome are masked for avoid annotation probleme. In addition this workflows can perform a illumina assembly with ABySS using différent value of kmere.
Last synced at: 7 months ago - Stars: 2 - Forks: 0
phim/sravel/EffiCAZ
Annotation of virulence factor of fungi (Effector , Cazyme ...)
Last synced at: 7 months ago - Stars: 1 - Forks: 0
