Stars
DNAfrags is a tool to filter reads in BAM files by fragment length and genome position
Add biological annotations to variants in a given VCF file.
Nanopore demultiplexing, QC and alignment pipeline
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Efficient phylogenetic clustering of viral sequences
Phylotype your strains using Clermont's 2013 method: ezclermont.org
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
antunderwood / nf-core-bactmap
Forked from nf-core/bactmapA mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
helper scripts for submission to ena (microbial + sarscov2) and gisaid (sarscov2 only)
Cross-platform software to draw phylogenetic trees
A python implementation of the joint ancestral state reconstruction algorithm of Pupko et al
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
snipit: summarise snps relative to your reference sequence
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
Nextflow workflow syntax highlighting and snippets for Sublime Text 4
Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
The ARTIC field bioinformatics pipeline
Rapid determination of appropriate reference genomes.