607 Open source projects that are alternatives of or similar to simplesam

pythonic wrapper for htslib

A D library for computational biology and bioinformatics

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pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Frequently used commands in bioinformatics

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

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

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Deep learning infrastructure for bioinformatics

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GenomeTools genome analysis system.

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

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

🔬 BEDOPS: high-performance genomic feature operations

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

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

A fast whole-genome aligner based on de Bruijn graphs

A faster lmm for GWAS. Supports GPU backend.

An interactive web tool for quality control of DNA sequencing data

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

A collection of scripts and notes related to genomics and bioinformatics

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

Haplotype VCF comparison tools

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

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

NGLess: NGS with less work

nim wrapper for htslib for parsing genomics data files

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

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

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

Reads simulator

Rapid large-scale prokaryote pan genome analysis

A genome browser that shows long reads and complex variants better

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

Intuitive local web frontend for the BLAST bioinformatics tool

A powerful open source data warehouse system

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

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

JavaScript VisualizationTools

Official git repository for Biopython (originally converted from CVS)

cython + htslib == fast VCF and BCF processing

Syntax highlighting for computational biology

Toolkit for preparing genomes for submission to NCBI

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

Model and predict short DNA sequence features with neural networks

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

An ultrafast memory-efficient short read aligner

My bioinfo toolbox