gitlab.mbb.univ-montp2.fr
seaconnect/clean-fastq
A workflow designed to clean SINGLE-END fastq files
Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
edna/reference_database
Collection of scripts to build a reference database.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/worldmap_fish_genetic_diversity
Global determinants of freshwater and marine fish genetic diversity
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/primer_design
How to design a primer ?
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
intrapop/assemble_mitogenome
Collections of mitogenome assembly methods from whole genome sequencing data
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
saltstack-formulas/get_d_states
SaltStack formula to get process in D states.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/metabarcoding_data_simulations
Simulations of metabarcoding data from fish 12S Teleo1
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
saltstack-formulas/check_disks
SaltStack check_disks formula. Used by jsonreader2.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
bev/seascape_course_cloud
Required dependencies for the Seascape genomics class.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
seaconnect/annotationvariant
Seek positions of variants onto genome and check if they are on an annotated region e.g. coding region. Then seek the proteic function of the gene
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
saltstack-formulas/set_grains
A SaltStack formula to setup roles and pool grains based on the subnet(s) and hostname.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
mbb/subwaw
A web interface to design and run workflows as part of MBB-workflows framework
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
mbb/mbb_micro-primers
Fork to change files copying to simple links
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
saltstack-formulas/check_services
A SaltStack formula to check a list of services from pillar data.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
seaconnect/seaConnect--dataPrep
Scripts to prepare SNP data for analysis
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/snakemake_rapidrun_data_test
metabarcoding test data for snakemake rapidrun workflow
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/edna_intra_pipeline_comparison
This project aims to compare twelve bioinformatics pipelines based on five existing metabarcoding programs to make recommendations for data management in intraspecific variability studies using environmental DNA.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/sexual_palinurus_elephas
Analysis around palinurus ortus
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
grenouille_rousse/mitochondrion
Check available resources on mitochondrion and assembly
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/primers_specificity_mismatchplot
Visualization of the specificity of designed primers with mismatch plot
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
mbb/dnabushmeat
Code used by https://mbb.univ-montp2.fr/MBB/dnabushmeat
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
mbb/modulefiles
mirror of modulefiles repository on gitlabpriv (but there is no reason to let this repository in a private state)
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/custom_reference_database
scripts to create our own reference database with our own sequences only and using the NCBI taxonomy
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
courses/ncbi_entrez
Understand the NCBI database and to do request using `entrez` and `Rentrez`
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/primer_specificity_ecopcr
This project permits to check the specificity of already designed primers.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/query_metabarcoding_data
a shiny application to query information about our metabarcoding data
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
courses/workshop_git
Using Git in a team: learn and practice Git and discover its features !
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/test_metabarcoding_data
data test to check metabarcoding workflow processing
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
grenouille_rousse/probedesign
Useful information about Rana temporaria genome and mitogenome. RADseq digestion, choices of restriction enzyme, RNA probe design
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/swarm_and_obitools
This project is based on the idea that gathering similar sequences allows to faithfully study them by eliminating sequences generated from PCR or NGS errors.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/beginning_obitools
The first step to begin with obitools and Bash
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/only_obitools
This project presents a pipeline based on OBITools commands in order to eliminate sequences interpreted as coming from PCR errors and to assign each remaining sequence to a taxon thanks to a reference database.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/dada2_and_obitools
This project has for goal to filtrate efficiently eDNA sequences after PCR amplification and NGS, in order to eliminate the false sequences generated by these technologies.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/tutorial_metabarcoding_data
Data for the tutorial on how to analyze DNA metabarcoding data produced on Illumina sequencers
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/snakemake_rapidrun_obitools
DNA Metabarcoding analyse on RAPIDRUN data with OBITOOLS encapsulated in SNAKEMAKE
Last synced at: about 1 year ago - Stars: 0 - Forks: 2
reservebenefit/occurence_freshwater_marine_species
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/snakemake_rapidrun_swarm
OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/benchmark_pipelines
Comparison of multiple bioinformatic programs for each step of eDNA analysis
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
seaconnect/ddocent_radseq
GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/worldmap_genetic_diversity_2
Here we go again to investigate genetic diversity patterns at different scale
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/snps_statistics
number of SNPs, distance between consecutive loci (in bp) and number of SNPs located on a coding region for each species
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
intrapop/primer-design
design primers for intrapopulation metabarcoding
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/webapp_marine_worldmap_bold
web-app interface investigating database Barcode of Life [BOLD](http://www.boldsystems.org/) geo referenced mitochondrial DNA barcode.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/genomic_resources_for_med_fishes
Codes for the paper : "Genomic resources for Mediterranean fishes"
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
aker/beetgenomeenvironmentassociation
Codes Pierre-Edouard Guerin wrote for the scientific paper "Predicting genotype environmental range from genome–environment associations"
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
mmassaviol/mbb_mqc_plugin
Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
bev/ffq
A tool designed to provide preprocessing for FASTQ files. This tool is developed in C++
Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
bev/singularity_hub
Singularity Container Registry made by [BEV](https://www.cefe.cnrs.fr/fr/recherche/bc/bev) team
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
bev/genbar
An approach to identify genetic boundaries between populations using individual spatial co-ordinates and unlinked codominant markers.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/genome_assemblies_collection
A collection of scripts used to do genome assemblies from raw sequencing data
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
reservebenefit/environmental_assign_data
Rscripts and link to our server to download and assign environmental data to sample according to their coordinates
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
mbb/singularity-local-recipes
Formulas for our local clusters.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
mbb/CroCo
A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification
Last synced at: about 1 year ago - Stars: 0 - Forks: 1
mbb/doc_user
gitbooks des formations et toutes les documentations publiques
Last synced at: about 1 year ago - Stars: 0 - Forks: 0