569 Open source projects that are alternatives of or similar to Bowtie

Python library to facilitate genome assembly, annotation, and comparative genomics

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Genomics Extension for SQLite

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Scripts to download genomes from the NCBI FTP servers

A collection of publications on comparison of high-throughput sequencing technologies.

Ten Quick Tips for Deep Learning in Biology

Official git repository for Biopython (originally converted from CVS)

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Code examples of fast and simple k-mer counters for tutorial purposes

Haplotype VCF comparison tools

A tool to circularize genome assemblies

The next version of bwa-mem

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

dysgu-SV is a collection of tools for calling structural variants using short or long reads

NGLess: NGS with less work

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Compute N50/NG50 and auN/auNG

A package for designing compact and comprehensive capture probe sets.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Toolkit for preparing genomes for submission to NCBI

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Assembling the cause of phenotypes and genotypes from NGS data

A curated list of awesome bioinformatics software.

Provide R access to the NCI Genomic Data Commons portal.

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

A fast 23andMe genome text file parser, now superseded by arv

De novo assembly based variant calling pipeline for Illumina short reads

Antimicrobial Resistance Identification By Assembly

A React web application to query and share any PostgreSQL database.

annotate a VCF with other VCFs/BEDs/tabixed files

An open source platform for managing and analyzing biomedical big data

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A collection of scripts and notes related to genomics and bioinformatics

Java utilities for Bioinformatics

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Example client programs for Saphetor's VarSome annotation API

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Efficient variant-call data storage and retrieval library using the TileDB storage library.

A fast whole-genome aligner based on de Bruijn graphs

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Intuitive local web frontend for the BLAST bioinformatics tool

A comprehensive library for computational molecular biology

MISO: An open-source LIMS for NGS sequencing centres

Cuneiform distributed programming language

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

Fast multi-line FASTA/Q reader in several programming languages

Simple simulation of single-cell RNA sequencing data

A curated list of resources for learning bioinformatics.

Python package for graph neural networks in chemistry and biology

Curated (meta)list of resources for Biology.

Annotated data.

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

ECG classification programs based on ML/DL methods

A repository for setting up a RNAseq workflow

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Single cell perturbation prediction

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.