TsumaR

CursorSpectrum

A software which enables interactive interpretation of mapping Raman spectra

vclean

viral-protein-function-plm

Viral protein family functional prediction using protein language models

vcfbub

use variant nesting information to flter overlapping sites from vg deconstruct output

gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

vg

tools for working with genome variation graphs

pggb

the pangenome graph builder

SuperPang

Non-redundant pangenome assemblies from multiple genomes or bins

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

fetchMGs.pl

svim-asm

Structural Variant Identification Method using Genome Assemblies

cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

ccfind

ccfind - circular complete genome finder with clues of terminal redundancy

vamb

Variational autoencoder for metagenomic binning

smaglinker

SMAGLinker is bioinformatic tool that can integrate SAG and MAG to reconstruct qualified microbial genomes.

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

simka

Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.

reflex

🕸️ Web apps in pure Python 🐍

pharokka

fast phage annotation program

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

Sniffles

Structural variation caller using third generation sequencing

serratus

Ultra-deep search for novel viruses

taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling

genomad

geNomad: Identification of mobile genetic elements

CAT_pack

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes

MAGRE

phanta

Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes

awesome-phages

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.