⚡ ♒ Rapid prokaryotic genome annotation

Automatically exported from code.google.com/p/cdhit

✂️ ⚡ Rapid haploid variant calling and core genome alignment

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Rapid large-scale prokaryote pan genome analysis

🔬 ♌ Bacterial ribosomal RNA predictor

🆔 Scan contig files against PubMLST typing schemes

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

NOVOPlasty - The organelle assembler and heteroplasmy caller

🌳 Create a tree using Mash distances

🐉 🪰 Assemble bacterial isolate genomes from Nanopore reads

A toolbox for pangenome analysis and threshold evaluation.

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)

Filter SAM file for soft and hard clipped alignments

An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis c…

Miscellaneous Perl scripts from 20 years in microbial bioinformatics

Variant calling pipeline designed for Q20+ ONT long-reads

NCBI Pathogen Detection Portal toolkit

workflows for GitHub Actions

estimate MLST with hashes

a very superficial attempt to replace nextflow's java engine with perl