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Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with sequencing

A curated list of projects in awesome lists tagged with sequencing .

https://github.com/google/deepvariant

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

bioinformatics deep-learning deep-neural-network deepvariant dna genome genomics machine-learning ngs science sequencing tensorflow

Last synced: 13 May 2025

https://github.com/bitfieldaudio/OTTO

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

audio audio-processing music raspberry-pi sequencing synth synthesizer ui-design

Last synced: 23 Apr 2025

https://github.com/bitfieldaudio/otto

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

audio audio-processing music raspberry-pi sequencing synth synthesizer ui-design

Last synced: 15 May 2025

https://github.com/OpenGene/fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi

Last synced: 07 May 2025

https://github.com/opengene/fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi

Last synced: 23 Jan 2026

https://github.com/broadinstitute/gatk

Official code repository for GATK versions 4 and up

bioinformatics dna gatk genome genomics ngs science sequencing spark

Last synced: 14 May 2025

https://github.com/brentp/mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

coverage depth exome genome hacktoberfest nim nim-lang sequencing wgs

Last synced: 11 Mar 2025

https://github.com/hemberg-lab/scRNA.seq.course

Analysis of single cell RNA-seq data course

bookdown course r scrna-seq scrna-seq-analysis sequencing

Last synced: 06 May 2025

https://github.com/xebia-functional/fetch

Simple & Efficient data access for Scala and Scala.js

cats concurrency data data-fetching monads monix parallelism scala scala-js sequencing

Last synced: 11 Jan 2026

https://github.com/milaboratory/mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

10x antibody bioinformatics immunology rep-seq rna-seq sequencing single-cell t-cell t-cell-receptor

Last synced: 20 Jan 2026

https://github.com/ideoforms/isobar

A Python package 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 actions.

algorithmic-composition composition midi music sequencing

Last synced: 14 Jul 2025

https://github.com/google/deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

bioinformatics deep-learning deepsomatic dna genome genomics machine science sequencing somatic-mutations somatic-variants

Last synced: 06 Mar 2026

https://github.com/biocommons/hgvs

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

bioinformatics genome-analysis genomics hgvs sequencing transcript variant-analysis variation

Last synced: 11 Mar 2026

https://github.com/samtools/htsjdk

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

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 14 May 2025

https://github.com/wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

bioinformatics blast genomics genomics-visualization hacktoberfest javascript ruby sequence-alignment sequencing visualization

Last synced: 15 May 2025

https://github.com/chanzuckerberg/shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

assembly de-novo dna long-read nanopore pacbio sequencing

Last synced: 05 May 2025

https://github.com/nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

clade clades coronavirus covid covid-19 covid19 dna influenza ncov neherlab next-generation-sequencing nextstrain research rna sars-cov-2 science sequences sequencing strain virus

Last synced: 15 Apr 2026

https://github.com/sortmerna/sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

alignment bioinformatics cpp metatranscriptomics ngs python sequencing

Last synced: 06 Apr 2025

https://github.com/igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

bioinformatics dna fast5 fasta fastq genomics gtf illumina nanopore science sequencing vcf workflow

Last synced: 21 Jan 2026

https://github.com/ugeneunipro/ugene

UGENE is free open-source cross-platform bioinformatics software

bioinformatics cpp cross-platform dna msa ngs pipeline qt5 science sequencing ugene workflow

Last synced: 04 Mar 2026

https://github.com/opengene/afterqc

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

adapter-trimming bioinformatics error fastq filtering ngs overlap qc quality-control sequencing trimming

Last synced: 07 Mar 2026

https://github.com/OpenGene/AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

adapter-trimming bioinformatics error fastq filtering ngs overlap qc quality-control sequencing trimming

Last synced: 05 May 2025

https://github.com/LooseLab/readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers

adaptive-sampling bioinformatics genomics ont oxford-nanopore sequencing

Last synced: 06 May 2025

https://github.com/mlin/GenomicSQLite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 16 May 2025

https://github.com/mlin/genomicsqlite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 05 Apr 2025

https://github.com/rajewsky-lab/mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data

analysis mapping microrna mirna prediction quantification sequencing smallrna

Last synced: 02 Feb 2026

https://github.com/KairosResearchLab/vvvv.Kairos

A complete framework for data control and composition in the vvvv visual programming environment.

animation automation blending composition control-systems data-layer interpolation sequencing timeline vl vvvv

Last synced: 07 Aug 2025

https://github.com/frederickhuanglin/ancombc

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

ancom ancombc ancombc2 correlation differential-abundance-analysis microbiome normalization secom sequencing

Last synced: 20 Oct 2025

https://github.com/opengene/gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

bioinformatics consensus deduplication deep-sequencing duplex duplex-sequencing duplication ngs sequencing sequencing-error sequencing-noise somatic

Last synced: 20 Aug 2025

https://github.com/telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

bioconda bioinformatics bioinformatics-tool fasta fastq genomics ngs sequencing

Last synced: 21 Oct 2025

https://github.com/OpenGene/fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

2019-ncov bioinformatics coronavirus covid covid-19 hcov meta-genomics microbial-sequences mngs ngs sars-cov-2 sequencing viral viral-infectious-diseases virus visualization

Last synced: 09 May 2025

https://github.com/opengene/fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

2019-ncov bioinformatics coronavirus covid covid-19 hcov meta-genomics microbial-sequences mngs ngs sars-cov-2 sequencing viral viral-infectious-diseases virus visualization

Last synced: 10 Apr 2025

https://github.com/zya/beet.js

Polyrhythmic Sequencer library for Web Audio API.

audio js library music sequencing webaudio webaudio-api

Last synced: 24 Oct 2025

https://github.com/OpenGene/gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

bioinformatics consensus deduplication deep-sequencing duplex duplex-sequencing duplication ngs sequencing sequencing-error sequencing-noise somatic

Last synced: 09 May 2025

https://github.com/robertaboukhalil/fastq.bio

An interactive web tool for quality control of DNA sequencing data

bioinformatics fastqc genomics sequencing wasm webassembly

Last synced: 05 Mar 2025

https://github.com/LiuLabUB/HMMRATAC

HMMRATAC peak caller for ATAC-seq data

atac-seq machine-learning peak-caller peak-detection sequencing

Last synced: 10 May 2025

https://github.com/tobiasrausch/wally

Wally: Visualization of aligned sequencing reads and contigs

alignment assembly contigs genomics mapping plotting sequencing sequencing-data visualization

Last synced: 13 Apr 2025

https://github.com/algbio/ggcat

Compacted and colored de Bruijn graph construction and querying

bioinformatics bioinformatics-pipeline de-novo-assembly debruijn-graph genome-assembly rust sequencing

Last synced: 06 Feb 2026

https://github.com/tobiasrausch/atacseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

atac-seq atac-seq-pipeline chromatin next-generation-sequencing nucleosome-positioning peak-detection sequencing

Last synced: 18 Mar 2026

https://github.com/eth-sri/astarix

AStarix: Fast and Optimal Sequence-to-Graph Aligner

edit-distance graph-alignment sequencing shortest-paths

Last synced: 03 Apr 2026

https://github.com/igordot/sns

Analysis pipelines for genomic sequencing data

analysis atac-seq bioinformatics dna genomics illumina nyu pipeline rna-seq rrbs sequencing wes wgbs wgs

Last synced: 21 Jan 2026

https://github.com/0xTCG/aldy

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

adme allele bioinformatics cyp2d6 genotype illumina pgrnseq sequencing

Last synced: 14 Mar 2025

https://github.com/robertaboukhalil/ginkgo

Cloud-based single-cell copy-number variation analysis tool

bioinformatics sequencing single-cell-genomics

Last synced: 29 Apr 2025

https://github.com/biocommons/biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

bioinformatics genome-analysis genomics sequencing variant-analysis variation

Last synced: 11 Mar 2026

https://github.com/opengene/uniquekmer

Generate unique KMERs for every contig in a FASTA file

bioinformatics fasta kmer ngs sequencing unique virus

Last synced: 10 Apr 2025

https://github.com/refresh-bio/colord

A versatile compressor of third generation sequencing reads.

bioinformatics compression fastq-files genomics long-reads oxford-nanopore pac-bio sequencing

Last synced: 04 Apr 2026

https://github.com/walaj/bxtools

Tools for analyzing 10X Genomics data

genomics sequencing tenxgenomics

Last synced: 21 Jan 2026

https://github.com/lpantano/seqcluster

small RNA analysis from NGS data

mirna report sequencing smallrna trna

Last synced: 10 Feb 2026

https://github.com/microsud/microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.

16s amplicon core-microbiome metagenomics microbial-communities microbiome microbiome-analysis qc-pipeline sequencing

Last synced: 26 Oct 2025

https://github.com/edinburgh-genome-foundry/primavera

:cherry_blossom: Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.

dna-assembly primer-design sequencing synthetic-biology

Last synced: 05 Sep 2025

https://github.com/zhanxw/seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

annotation bcf bgen meta-analysis next-generation-sequencing plink sequencing tabix vcf workflow

Last synced: 18 Feb 2026

https://github.com/opengene/defq

Please switch to https://github.com/OpenGene/defastq

demultiplexing demux dual-index fastq illumina index sequencing split

Last synced: 10 Apr 2025

https://github.com/jamiebuilds/graph-sequencer

Sort items in a graph using a topological sort while resolving cycles with priority groups

adjacency-lists cycles graph priority-list sequencing sorting

Last synced: 15 Mar 2025

https://github.com/cdcgov/tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

azure bioinformatics conda docker genbank genetics liftoff metadata mpox ncbi nextflow nf-tower pipeline python rna-seq scicomp sequencing singularity sra vadr

Last synced: 15 Apr 2025

https://github.com/maragkakislab/samql

SQL-like query language for the SAM/BAM file format

bam bioinformatics go sam sequencing sql

Last synced: 19 Apr 2025

https://github.com/hasindu2008/cornetto

adaptive genome assembly using nanopore sequencing

assembly genome nanopore sequencing

Last synced: 17 Apr 2026

https://github.com/corneliusroemer/desh-data

Sequence lineage information extracted from RKI sequence data repo

dataset germany lineages pangolin robert-koch-institut sars-cov-2 sequencing

Last synced: 13 Apr 2025

https://github.com/biocommons/bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

bioinformatics genome-analysis genomics sequencing variant-analysis variation

Last synced: 11 Mar 2026

https://github.com/greenelab/pdx_exomeseq

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

analysis cancer methodology mutation notebook pancreatic-cancer pdx pipeline sequencing wes

Last synced: 31 Jan 2026

https://github.com/snijderlab/stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling

antibody mass-spectrometry sequencing

Last synced: 24 Aug 2025

https://github.com/openpaul/fqless

less like viewer for fastq files

biology fastq fastq-files ngs sequencing unix

Last synced: 17 Jan 2026

https://github.com/jamesseanwright/nanotunes

A small music format and an accompanying implementation using OscillatorNode

music oscillatornode sequencing synthesis web-audio

Last synced: 12 Apr 2025

https://github.com/wglab/nanorepeat

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

bioinformatics genome-analysis genomics nanopore-sequencing pacbio-sequencing repeat-detection sequencing short-tandem-repeats

Last synced: 17 Jan 2026

https://github.com/lhqing/cemba_data

Mapping pipeline for snmC-seq based technologies.

methylation pipeline sequencing single-cell snmc-seq snmc-seq2 snmct-seq

Last synced: 01 Apr 2026

https://github.com/pdimens/harpy

Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!

bioinformatics haplotype linked-reads pipeline sequencing variant-calling

Last synced: 03 Feb 2026

https://github.com/seandavi/ngcgh

Tools for producing pseudo-cgh of next-generation sequencing data

bioinformatics cancer-genomics genomics python sequencing

Last synced: 09 Oct 2025

https://github.com/sydney-informatics-hub/fastq-to-bam

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

bioinformatics bwa-mem gatk-bestpractices mapping ngs sequencing

Last synced: 12 Jul 2025

https://github.com/tobiasrausch/nrex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

alignment germline mutations sequencing somatic-mutations somatic-variants structural-variation variant-calling

Last synced: 10 Jul 2025

https://github.com/nebiolabs/ampseer

Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.

pcr sars-cov-2 sequencing targeted-sequencing

Last synced: 04 Mar 2026

https://github.com/fls-bioinformatics-core/auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data within the Bioinformatics Core Facility at the University of Manchester

10xgenomics automation bioinformatics fastq-files illumina next-generation-sequencing pipeline qc sequencing

Last synced: 23 Jan 2026

https://github.com/mutwo-org/mutwo.core

core library of mutwo: event based library for composing music or other time-based arts in python

algorithmic-composition composition creative-coding csound generative-art midi music notation sequencing

Last synced: 16 Jan 2026

https://github.com/vegaprotocol/wendy

Wendy, the good little fairness widget

blockchain fairness ordering sequencing

Last synced: 15 Aug 2025

https://github.com/bu-isciii/taranys

cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.

bacterial-genomes cgmlst mlst outbreak-data-analysis outbreak-detection sequencing wgmlst

Last synced: 05 Apr 2025

https://github.com/ucsd-ccbb/c-view

This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.

epidemiology sequencing viral-genomics

Last synced: 12 Jul 2025

https://github.com/fulcrumgenomics/fgumi

High-performance UMI tools for NGS data analysis

bioinformatics consensus-calling duplex-sequencing genomics ngs rust sequencing umi

Last synced: 28 Feb 2026