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

No description or website provided.

Development repository for the Bioconductor package 'mixOmics '

Curated list of bioinformatics formats and publications

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

A library for generating an interactive SVG visualization of CWL workflows

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

A robust and fast clustering method for amplicon-based studies

List of Computer Science courses with video lectures.

📊 Identify cell types and pathways affected by genetic risk loci.

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

MOLGENIS - for scientific data: management, exploration, integration and analysis.

C library for high-throughput sequencing data formats

Emperor a tool for the analysis and visualization of large microbial ecology datasets

Examples using Clustergrammer2 to explore high-dimensional datasets.

VirNet: A deep attention model for viral reads identification

Yet Another Chimeric Read Detector

Syntax highlighting for computational biology

Biostar Q&A

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Toolset for SV simulation, comparison and filtering

parallel fastq-dump wrapper

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

BWK awk modified for biological data

Mapping-Assisted Targeted-Assembly for Metagenomics

Lightweight Iterative Gene set Enrichment in R

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Inference of switch-like differential expression along single-cell trajectories

Tools and databases for analyzing HLA and VDJ genes.

exploratory and interactive microbiome analyses based on heatmaps

APBS - software for biomolecular electrostatics and solvation

Find causal cell-types underlying complex trait genetics

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

React rerelease of MSAViewer

RADseq Data Exploration, Manipulation and Visualization using R

A curated list of awesome Bioinformatics libraries and software.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

An efficient FASTQ manipulation suite

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Read DNA sequences from colourful Microsoft Word documents

Fast large scale matrix visualization for the web.

Versatile open-source tool for microbiome analysis

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

MMseqs2: ultra fast and sensitive search and clustering suite

Create regional association plots from GWAS or meta-analysis

UGENE is free open-source cross-platform bioinformatics software

A computational library for learning and evaluating biological knowledge graph embeddings

GeneValidator: Identify problems with predicted genes

Workflow Description Language - Specification and Implementations

code for reading and processing Allen Institute for Brain Science data

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

d3 library to build circular graphs

Post-analysis of immune repertoire sequencing data

Bioinformatics containers

A cross-platform command-line tool for executing jobs in parallel

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Python library to handle Gene Ontology (GO) terms

C++ library and cmdline tools for parsing and manipulating VCF files