Vileu's Stars
rstudio/cheatsheets
Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.
OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
samtools/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
ncbi/sra-tools
SRA Tools
COMBINE-lab/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
DerrickWood/kraken2
The second version of the Kraken taxonomic sequence classification system
weizhongli/cdhit
Automatically exported from code.google.com/p/cdhit
eggnogdb/eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
marbl/Krona
Interactively explore metagenomes and more from a web browser.
hyattpd/Prodigal
Prodigal Gene Prediction Software
bxlab/metaWRAP
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
Ecogenomics/CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
jenniferlu717/Bracken
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
kevinsblake/NatParksPalettes
Color palette package inspired by National Parks
conda-incubator/conda-tree
conda dependency tree helper
BinPro/CONCOCT
Clustering cONtigs with COverage and ComposiTion
YongxinLiu/EasyMicrobiome
HadrienG/tutorials
:books: Various bioinformatics tutorials
castelao/seabird
Python parser for Sea-Bird CTD outputs, usually .cnv files.
Linwei-Wu/warming_soil_biodiversity
mgtools/MinPath
MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
EMSL-Computing/CoreMS-Portal
EMSL-Computing/Day3-EMSL-SummerSchool-2022
microbiomedata/enviroMS
ramalok/mitags_extraction_protocol
mitags extraction protocol
clagovaldivia/genome-project
danczakre/EMSL2022_Visualization
Contains all of the files and scripts necessary to participate in the EMSL Summer School 2022 Visualization walkthrough
andreamentges/functional-diversity-index
Calculating functional molecular diversity of marine dissolved organic matter in MATLAB
nikhilg123/Module_5_metagenome_assembly-MAGs
EricRaes/Time-series-Analyses
Code for plotting the figures in the marine time-series manuscript