Stars
a short-read polishing tool for long-read assemblies
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
ATLAS - Three commands to start analyzing your metagenome data
Tool for fully-automated inference of species trees from raw genome assemblies
gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
Classify metagenomic contigs as eukaryotic or prokaryotic
Eukfinder: A pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and …
Automatically exported from code.google.com/p/cdhit
PSAURON is a machine learning model for rapid assessment of protein coding gene annotation
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
alignment-free coverage calculation for metagenomic binning >100 times faster
geNomad: Identification of mobile genetic elements
Python packaging and dependency management made easy
🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies
CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of regulatory elements.
🦠 A tool for identifying and analyzing functions in microbial genomes.
A Rust library providing fully dynamic sets of k-mers with high locality
Classifier for metagenomic sequences using FM-index with run-block compressed BWT.
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes