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

Fast alignment and preprocessing of chromatin profiles

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Scripts to download genomes from the NCBI FTP servers

Predict plasmids from uncorrected long read data

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Antimicrobial Resistance Identification By Assembly

A cool place to store your Hi-C

GCP Essentials for Bioinformatics Researchers

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

A tool to circularize genome assemblies

A versatile pairwise aligner for genomic and spliced nucleotide sequences

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Bayesian haplotype-based mutation calling

Deep learning infrastructure for bioinformatics

Ten Quick Tips for Deep Learning in Biology

GenomeTools genome analysis system.

nim wrapper for htslib for parsing genomics data files

🔬 BEDOPS: high-performance genomic feature operations

Proof-of-concept seq-to-graph mapper and graph generator

An ultrafast memory-efficient short read aligner

Intuitive local web frontend for the BLAST bioinformatics tool

Official git repository for Biopython (originally converted from CVS)

A simple command-line tool to download data from Joint Genome Institute databases

Data intensive science for everyone.

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

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

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

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

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Provide R access to the NCI Genomic Data Commons portal.

Toolkit for preparing genomes for submission to NCBI

A faster lmm for GWAS. Supports GPU backend.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

A modern genome browser built with JavaScript and HTML5.

Tools to process and analyze deep sequencing data.

Genomics Extension for SQLite

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

compacted de Bruijn graph construction in low memory

Create regional association plots from GWAS or meta-analysis

Exact Tandem Repeat Finder (not a TRF replacement)

SquiggleKit: A toolkit for manipulating nanopore signal data

Characterization of Germline variants

GeneValidator: Identify problems with predicted genes

🌈Scaffold genome sequence assemblies using linked read sequencing data

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Post-analysis of immune repertoire sequencing data

EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Comprehensive toolkit for generating various numerical features of protein sequences

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

A friendly next-generation interface for Genomic data discovery powered by InterMine

Snakemake-based workflow for detecting structural variants in WGS data

Randomly subsample sequencing reads to a specified coverage

GO enrichment with python -- pandas meets networkx