Jorge Langa's repositories
smsk_trinotate
Snakemake workflow to run transdecoder + trinotate
smsk_popoolation
Snakemake pipeline for Popoolation and Popoolation2
smsk_selection
Snakemake project to predict orthogroups and find patterns of postive selection with orthofinder and fastcodeml
smsk_gatk_germline
Snakemake workflow to perform GATK's best practices for Germline SNP & Indel Discovery in Whole Genome and Exome Sequence
2023-mer_metagenomics
Tutorial and assignments for the course Marine Genomics at IMBRSEA, Plentzia
smsk_tuxedo2
snakemake files of the tuxedo v2 pipeline from Pertea et al 2016
2023-mer_metagenomics_exercises
Exercises for the metabarcoding part of the Marine Genomic Resources class
2024-mer_metagenomics
Tutorial and assignments for the course Marine Genomics at IMBRSEA, Plentzia
ansible-role-slurm
For installing and configuring SLURM - Simple Linux Utility for Resource Management
bioconda-recipes
Conda recipes for the bioconda channel.
biopython.github.io
Source of biopython.org website, migrated from MediaWiki
cache
Cache dependencies and build outputs in GitHub Actions
exfi-docker
Build a Docker container with all the tools to execute exfi
hillR
An R pakage to calculate diversity through Hill Numbers
ht_quant
Repository containing bioinformatic code for macro-scale host transcriptomic data processing
pyrollinghash
Cython wrapper of the rollinghashcpp C++ repo
smsk_exfi_paper
snakemake pipeline to get the results from the exfi paper
smsk_kraken2_pathogens
Find and quantify pathogens with kraken2 and bowtie2 as in Lu et al 2022
smsk_sketch
Compare sequencing runs and genomes with sourmash, skmer and sylph sketches