1009 Open source projects that are alternatives of or similar to PHAT

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Assembling the cause of phenotypes and genotypes from NGS data

Official code repository for GATK versions 4 and up

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

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

🚦 Run Picard on BAM files and collate 90 metrics into one file.

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

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Analysis pipelines for sequencing data

UGENE is free open-source cross-platform bioinformatics software

Data intensive science for everyone.

Utilities for analyzing next generation sequencing data.

R package for analyzing single-cell RNA-seq data

A package for designing compact and comprehensive capture probe sets.

A fast 23andMe genome text file parser, now superseded by arv

Efficient pythonic random access to fasta subsequences

Java utilities for Bioinformatics

MMseqs2: ultra fast and sensitive search and clustering suite

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

A D library for computational biology and bioinformatics

Tools to process and analyze deep sequencing data.

Aggregate results from bioinformatics analyses across many samples into a single report.

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

LAMBDA – the Local Aligner for Massive Biological DatA

Parser and database to index the terpene profile of different strains of Cannabis from online databases

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

A robust model for quantitative comparison of ChIP-Seq data sets.

A fast whole-genome aligner based on de Bruijn graphs

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

NGLess: NGS with less work

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

C library for high-throughput sequencing data formats

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

(No maintenance) Detect gene fusion directly from raw fastq files

Remote protein homology detection suite.

SortMeRNA: next-generation sequence filtering and alignment tool

A collection of scripts and notes related to genomics and bioinformatics

Official git repository for Biopython (originally converted from CVS)

python Circos

DOM Text Based Multiple Sequence Alignment Library

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

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

Tools for working with genomic and high throughput sequencing data.

An easy-to-use way for running Galaxy workflows.

Rare variant test software for next generation sequencing data

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

Finds SNP sites from a multi-FASTA alignment file

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

Multi-sample somatic variant caller

Ultrafast sequence typing and gene detection from NGS raw reads

Improve the quality of a denovo assembly by scaffolding and gap filling

My bioinfo toolbox

Multilocus sequence typing by blast using the schemes from PubMLST

medical image visualization library and development toolkit

an R/shiny application for creation of Circos plot interactively

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

A simplified pipeline for ctDNA sequencing data analysis