xvazquezc's Stars
google-deepmind/alphafold
Open source code for AlphaFold.
ncbi/sra-tools
SRA Tools
malonge/RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
krassowski/complex-upset
A library for creating complex UpSet plots with ggplot2 geoms
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
kevinblighe/EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labeling
wwood/CoverM
Read coverage calculator for metagenomics
r-lib/waldo
Find differences between R objects
wwood/kingfisher-download
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
franciscozorrilla/metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
svalvaro/drawCell
R package to create cell pictures.
rpetit3/dragonflye
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
oschwengers/platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
arthurwelle/codehover
Hoverable HTML Table for Displaying Intermediary Code Results (e.g. Pipes)
bhattlab/lathe
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
mw55309/ideel
Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
agmcfarland/r_phylogenetics_worshop
Using ggtree to build phylogenetic trees
functional-dark-side/agnostos-wf
ohlab/GRiD
Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
fmenardo/Treemmer
Python tool to reduce size and redundancy of phylogenetic datasets
meglab-metagenomics/amrplusplus_v2
MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data
DavidBSauer/OGT_prediction
Scripts for calculating features and regression of prokaryote OGT
simonwhelan/Divvier
A program for divvying or partially filtering multiple sequence alignments
tyjo/coptr
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing
Tancata/phylo
Helper scripts for making phylogenies
marbl/binnacle
Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins
ndombrowski/Annotation_workflow
Workflow used to annotate genomes starting from the fasta files.
Psy-Fer/misc
Various scripts and how-to's related to bioinformatics, genomics, and nanopore sequencing
dspeth/ASM_clust
protein clustering using alignment score matrices