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

Seven Bridges Genomics aligner/caller debugging and analysis tools

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A collection of scripts and notes related to genomics and bioinformatics

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

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A powerful open source data warehouse system

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Flexible genotype query among 30,000+ samples whole-genome

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

Official git repository for Biopython (originally converted from CVS)

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An open-source toolkit for large-scale genomic analysis

Analysis pipelines for sequencing data

High-performance error correction for Illumina resequencing data

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Tools to work with variant call format files

A list of web-based interactive biological data visualizations.

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Genomic Data Retrieval with R

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

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`

Data intensive science for everyone.

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

Scalable genomic data analysis.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Scripts to download genomes from the NCBI FTP servers

Python package and CLI for whole-genome duplication related analyses

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

nim wrapper for htslib for parsing genomics data files

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

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

Python library to facilitate genome assembly, annotation, and comparative genomics

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

A fast and sensitive gapped read aligner

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

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.

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.