595 Open source projects that are alternatives of or similar to Somalier

The next version of bwa-mem

Java utilities for Bioinformatics

Snakemake-based workflow for detecting structural variants in WGS data

A tool to circularize genome assemblies

A fast and sensitive gapped 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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Bayesian haplotype-based mutation calling

Ten Quick Tips for Deep Learning in Biology

Reads simulator

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

A modern genome browser built with JavaScript and HTML5.

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

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

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

Intuitive local web frontend for the BLAST bioinformatics tool

JavaScript VisualizationTools

Official git repository for Biopython (originally converted from CVS)

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

A powerful open source data warehouse system

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

Toolkit for preparing genomes for submission to NCBI

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

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

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

Fast hash function for DNA sequences

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

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

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Provide R access to the NCI Genomic Data Commons portal.

Analysis pipelines for sequencing data

An open-access bioinformatics text

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

A curated list of awesome bioinformatics software.

A fast 23andMe genome text file parser, now superseded by arv

Bystro genetic analysis (annotation, filtering, statistics)

Official code repository for GATK versions 4 and up

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

De novo assembly based variant calling pipeline for Illumina short reads

A high-performance, Pythonic language for bioinformatics

Bayesian genotyper for structural variants

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

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

Efficient pythonic random access to fasta subsequences

Data intensive science for everyone.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Biological sequences for the julia language

pymzML - an interface between Python and mzML Mass spectrometry Files

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

Robust and efficient workflows using a simple language agnostic approach

An efficient FASTQ manipulation suite

Demonstrating best practices for bioinformatics command line tools

The START App: R Shiny Transcriptome Analysis Resource Tool

Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Global Biotic Interactions provides access to existing species interaction datasets