Awesome Open Source
Awesome Open Source
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The Top 32 Sequencing Open Source Projects
Categories
>
Science
>
Sequencing
Otto
⭐
2,243
Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
Deepvariant
⭐
2,202
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Gatk
⭐
988
Official code repository for GATK versions 4 and up
Fastp
⭐
951
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Galaxy
⭐
805
Data intensive science for everyone.
Fetch
⭐
448
Simple & Efficient data access for Scala and Scala.js
Mosdepth
⭐
373
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Htsjdk
⭐
218
A Java API for high-throughput sequencing data (HTS) formats.
Isobar
⭐
203
A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.
Sequenceserver
⭐
196
Intuitive local web frontend for the BLAST bioinformatics tool
Shasta
⭐
185
De novo assembly from Oxford Nanopore reads.
Snapatac
⭐
178
Analysis Pipeline for Single Cell ATAC-seq
Roary
⭐
174
Rapid large-scale prokaryote pan genome analysis
Afterqc
⭐
169
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Rnaseq Workflow
⭐
169
A repository for setting up a RNAseq workflow
Hgvs
⭐
137
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Artemis
⭐
135
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
Circlator
⭐
121
A tool to circularize genome assemblies
Ugene
⭐
107
UGENE is free open-source cross-platform bioinformatics software
Genomics
⭐
98
A collection of scripts and notes related to genomics and bioinformatics
Ariba
⭐
95
Antimicrobial Resistance Identification By Assembly
Genomicsqlite
⭐
87
Genomics Extension for SQLite
Truvari
⭐
83
Structural variant toolkit for VCFs
Beet.js
⭐
81
Polyrhythmic Sequencer library for Web Audio API.
Fastq.bio
⭐
74
An interactive web tool for quality control of DNA sequencing data
Mirdeep2
⭐
70
Discovering known and novel miRNAs from small RNA sequencing data
Gubbins
⭐
67
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Sns
⭐
42
Analysis pipelines for sequencing data
Migmap
⭐
38
HTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Awesome Sequencing Tech Papers
⭐
21
A collection of publications on comparison of high-throughput sequencing technologies.
Helmsman
⭐
19
highly-efficient & lightweight mutation signature matrix aggregation
Quagmir
⭐
9
A python-based isomiR quantification and analysis pipeline
1-32 of 32 projects
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