sequencing
There are 463 repositories under sequencing topic.
google/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
bitfieldaudio/OTTO
Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
broadinstitute/gatk
Official code repository for GATK versions 4 and up
galaxyproject/galaxy
Data intensive science for everyone.
ablab/spades
SPAdes Genome Assembler
hemberg-lab/scRNA.seq.course
Analysis of single cell RNA-seq data course
brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
xebia-functional/fetch
Simple & Efficient data access for Scala and Scala.js
twbattaglia/RNAseq-workflow
A repository for setting up a RNAseq workflow
ideoforms/isobar
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.
milaboratory/mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
ACEnglish/truvari
Structural variant toolkit for VCFs
r3fang/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
tmhglnd/mercury
A minimal and human-readable language and environment for the live coding of algorithmic electronic music.
samtools/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
chanzuckerberg/shasta
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
wurmlab/sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
biocommons/hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
sortmerna/sortmerna
SortMeRNA: next-generation sequence filtering and alignment tool
sanger-pathogens/Artemis
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
sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
sanger-pathogens/circlator
A tool to circularize genome assemblies
ZJUFanLab/scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
OpenGene/AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
nextstrain/nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
ugeneunipro/ugene
UGENE is free open-source cross-platform bioinformatics software
igordot/genomics
A collection of scripts and notes related to genomics and bioinformatics
HadrienG/InSilicoSeq
:rocket: A sequencing simulator
LooseLab/readfish
CLI tool for flexible and fast adaptive sampling on ONT sequencers
nickjcroucher/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
mlin/GenomicSQLite
Genomics Extension for SQLite
sanger-pathogens/ariba
Antimicrobial Resistance Identification By Assembly
tobiasrausch/alfred
BAM Statistics, Feature Counting and Annotation
rajewsky-lab/mirdeep2
Discovering known and novel miRNAs from small RNA sequencing data