gitlab.univ-nantes.fr / ecosysmic 16 Repositories
Project: Microbial Systems Ecology
ecosysmic/EcoSysMic-analysis
Contains all the analysis that were done on the EcoSysMic project (notebooks with figures).
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
ecosysmic/GeneAnnotation
Pipeline to predict and annotate genes in a list of genomes.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1
ecosysmic/BAMUtils
Tools to filter reads and estimate coverage statistics (depth and breadth) from BAM files.
Last synced at: 7 months ago - Stars: 0 - Forks: 0
ecosysmic/ReadMapping
Map reads from a list of samples (default: Tara Oceans dataset) to a set of genomes
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1
ecosysmic/CoverageEstimation
Compute coverage statistics from a list of indexed BAM files
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1
ecosysmic/SnakeCarveMe
Snakemake pipeline for metabolic network reconstruction for prokaryotes using CarveMe
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/SnakeMETANA
Pipeline to run SMETANA on communities of SBML models.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/MarineDB
Set of script to construct the MarineDB database (Marine MAGs + aquatic proGenomes)
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/marref
What commands were used to download and make usable the MarRef database.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/MarDB
What commands were used to download and make usable the MarDB database.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/dreplication
dRep implementation to dereplicate a genome database
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/SnakeGTDBTk
Snakemake implementation of GTDBTk. Automatically uses batches of genomes.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/SnakeCheckM
Pipeline that runs CheckM on a list of genomes recovered from metagenomes (MAGs).
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/MAGsDB
Utility to generate the database of MAGs used in the EcoSysMic project.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
ecosysmic/ProGenomes
Pipeline to download and manipulate data from the ProGenomes database (http://progenomes.embl.de/index.cgi)
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0