genome-analysis topic
mccortex
De novo genome assembly and multisample variant calling
Winnowmap
Long read / genome alignment software
rasusa
Randomly subsample sequencing reads
bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
intervene
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
positive-selection
Scripts and procedures for detecting positively selected genes and codons in primates
EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
ppsPCP
A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline
gwasTools
Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)