609 Open source projects that are alternatives of or similar to dna-traits

A curated list of awesome bioinformatics software.

A fast 23andMe DNA parser and inferrer for Python

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Efficient pythonic random access to fasta subsequences

Data intensive science for everyone.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Python and C++ code for reading and writing genomics data.

Analysis pipelines for sequencing data

Official git repository for Biopython (originally converted from CVS)

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

A package for designing compact and comprehensive capture probe sets.

Official code repository for GATK versions 4 and up

A collection of scripts and notes related to genomics and bioinformatics

Bayesian haplotype-based mutation calling

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Rapid large-scale prokaryote pan genome analysis

A curated list of bioinformatics bench-marking papers and resources.

Reads simulator

Fast alignment and preprocessing of chromatin profiles

A powerful open source data warehouse system

Intuitive local web frontend for the BLAST bioinformatics tool

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

cython + htslib == fast VCF and BCF processing

Deep learning infrastructure for bioinformatics

🔬 BEDOPS: high-performance genomic feature operations

JavaScript VisualizationTools

Assembling the cause of phenotypes and genotypes from NGS data

nim wrapper for htslib for parsing genomics data files

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

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

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

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

Ten Quick Tips for Deep Learning in Biology

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

GenomeTools genome analysis system.

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

A genome browser that shows long reads and complex variants better

An ultrafast memory-efficient short read aligner

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

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

Numerical Encoding for Human Genetic Variants

Provide R access to the NCI Genomic Data Commons portal.

Ultrafast sequence typing and gene detection from NGS raw reads

A package for designing activity-informed nucleic acid diagnostics for viruses.

tools for reading, writing, merging, and remapping SNPs

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

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Toolkit for preparing genomes for submission to NCBI

An open-access bioinformatics text

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

A faster lmm for GWAS. Supports GPU backend.

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

Predict plasmids from uncorrected long read data

Fast hash function for DNA sequences

Simple pure Python SAM parser and objects for working with SAM records

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

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

Fast and flexible ORF finder

Compute N50/NG50 and auN/auNG