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Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
A web application for finding and comparing bioinformatics training materials on GitHub and GitLab
An updated pipeline for pangenome investigation
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
pyngoST: multiple sequence typing of Neisseria gonorrhoeae for large assembly collections
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
NCBI Prokaryotic Genome Annotation Pipeline
Randomly subsample sequencing reads or alignments
A flexible pipeline for complete analysis of bacterial genomes
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
A toolkit to validate and consolidate antimicrobial resistance gene databases
🐉 🪰 Assemble bacterial isolate genomes from Nanopore reads
A Python script to count bacterial colonies on agar plates
A pipeline for running AMRfinderPlus and collating results into functional classes
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output inc…
✂️ ⚡ Rapid haploid variant calling and core genome alignment
NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
A tool for generating consensus long-read assemblies for bacterial genomes
A snakemake pipeline for SV analysis from nanopore genome sequencing