276 Open source projects that are alternatives of or similar to PHIST

A genome browser that shows long reads and complex variants better

Viral genomics analysis pipelines

cython + htslib == fast VCF and BCF processing

Intuitive local web frontend for the BLAST bioinformatics tool

Bayesian haplotype-based mutation calling

A DNA Sequence Alignment/Map (SAM) library for Clojure

Reads simulator

A tool for fast and accurate summarizing of variant calling format (VCF) files

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

Performant Pythonic GenomicRanges

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

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

xHLA: Fast and accurate HLA typing from short read sequence data

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

Genomics Workflows on AWS

Deep learning infrastructure for bioinformatics

JavaScript VisualizationTools

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

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

structural variant calling and genotyping with existing tools, but, smoothly.

An ultrafast memory-efficient short read aligner

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

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

MISO: An open-source LIMS for NGS sequencing centres

🔬 BEDOPS: high-performance genomic feature operations

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

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

Seven Bridges Genomics aligner/caller debugging and analysis tools

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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

A powerful open source data warehouse system

A WGS de novo assembler based on the FMD-index for large genomes

GenomeTools genome analysis system.

Easy genetic ancestry predictions in Python

Chromosome visualization for the web

Haplotype VCF comparison tools

Ten Quick Tips for Deep Learning in Biology

Find target sites for the miRNAs in genomic sequences

Rapid large-scale prokaryote pan genome analysis

Official git repository for Biopython (originally converted from CVS)

An open-source toolkit for large-scale genomic analysis

High-performance error correction for Illumina resequencing data

Tools to work with variant call format files

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

Genomic Data Retrieval with R

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

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

A Java API for high-throughput sequencing data (HTS) formats.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Python package and CLI for whole-genome duplication related analyses

nim wrapper for htslib for parsing genomics data files

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

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

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

SDK for GPU accelerated genome assembly and analysis

simuG: a general-purpose genome simulator

Genome-wide imputation pipeline

Population assignment analysis using R

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Fast large scale matrix visualization for the web.