Stars
A software which enables interactive interpretation of mapping Raman spectra
Viral protein family functional prediction using protein language models
use variant nesting information to flter overlapping sites from vg deconstruct output
Tools for manipulating sequence graphs in the GFA and rGFA formats
Non-redundant pangenome assemblies from multiple genomes or bins
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Structural Variant Identification Method using Genome Assemblies
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 - circular complete genome finder with clues of terminal redundancy
Variational autoencoder for metagenomic binning
SMAGLinker is bioinformatic tool that can integrate SAG and MAG to reconstruct qualified microbial genomes.
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
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
Structural variation caller using third generation sequencing
Ultra-deep search for novel viruses
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Scripts to download genomes from the NCBI FTP servers
motus - a tool for marker gene-based OTU (mOTU) profiling
geNomad: Identification of mobile genetic elements
CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.