Repositories list

• nar-paper

  Public
  GEAR web application snapshot

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• sabre

  Public
  Sequence Alignment Browser

  visualizationresearchgenomics+ 4

  visualizationresearchgenomicsdnaalignmentsequencegear-genomics

  JavaScript

  •

  GNU General Public License v3.0

  •11 fork•77 stars•00 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• halo

  Public
  Halo: Haplotype processor

  haplotypesalignmentbam+ 1

  haplotypesalignmentbamsingle-cell

  C++

  •

  GNU General Public License v3.0

  •11 fork•33 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• saint

  Public
  [WIP] saint (similarity hunter): Rapid DNA similarity search against entire genomes.

  JavaScript

  •11 fork•44 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• ancient

  Public
  Ancestry inference with convolutional neural networks

  machine-learningtensorflowsequencing+ 5

  machine-learningtensorflowsequencingancestryconvolutional-neural-networksancestry-researchsnp-genotypinggear-genomics

  Vue

  •

  GNU General Public License v3.0

  •22 forks•99 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• gearlog

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• apps-page

  Public
  GEAR home page

  websitegenomicscomputational-biology+ 4

  websitegenomicscomputational-biologyprimer-designsanger-chromatogramsgear-genomicssanger-sequencing

  Vue

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• dicey

  Public
  In-silico PCR, primer design and padlock design for in-situ sequencing

  primerpadlockpcr+ 7

  primerpadlockpcrampliconprimer-designamplicon-sequencinggear-genomicsin-silicosanger-sequencingin-situ-sequencing

  C++

  •

  GNU General Public License v3.0

  •33 forks•5454 stars•33 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• padlock

  Public
  Design padlock probes for in-situ sequencing

  genomicsprobesprobe-design+ 1

  genomicsprobesprobe-designin-situ-sequencing

  HTML

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• silica

  Public
  In-silico PCR amplification on complete genomes

  primerpcramplicon+ 4

  primerpcrampliconprimer-designgear-genomicsin-silicosanger-sequencing

  JavaScript

  •

  GNU General Public License v3.0

  •11 fork•1111 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• wily-dna-editor

  Public
  The Wily-DNA-Editor is a browser tool for plasmid assembly, reverse complements DNA, translates to protein code and calculates restriction digests maps.

  gear-genomics

  gear-genomics

  JavaScript

  •

  GNU General Public License v3.0

  •11 fork•1515 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• pearl

  Public
  Patching references via trace assemblies

  pcrsanger-chromatogramsgear-genomics+ 2

  pcrsanger-chromatogramsgear-genomicssanger-trace-alignmentsanger-sequencing

  JavaScript

  •

  GNU General Public License v3.0

  •33 forks•55 stars•55 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• wallyapp

  Public
  Frontend web application for wally to visualize aligned sequencing reads

  visualizationgenomicsalignment+ 2

  visualizationgenomicsalignmentgenomics-visualizationsequencing-data

  HTML

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• teal

  Public
  Sanger Trace Viewer

  tracepcrsanger-chromatograms+ 2

  tracepcrsanger-chromatogramssangergear-genomics

  JavaScript

  •

  GNU General Public License v3.0

  •22 forks•1010 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• sage

  Public
  Sanger Trace Alignment

  tracealignmentpcr+ 4

  tracealignmentpcrsanger-chromatogramschromatogramgear-genomicssanger-trace-alignment

  JavaScript

  •

  GNU General Public License v3.0

  •11 fork•44 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• tracy

  Public
  Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

  sequencingalignmentcrispr-analysis+ 12

  sequencingalignmentcrispr-analysisvariant-callingpcrtracycrispr-cas9sanger-chromatogramsindel-discoverychromatogram+ 5

  C++

  •

  BSD 3-Clause "New" or "Revised" License

  •2323 forks•122122 stars•77 issues•11 pull request•Updated Apr 7, 2026Apr 7, 2026

• indigo

  Public
  Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

  sequencingvariantsalignment+ 13

  sequencingvariantsalignmentcrispr-analysisindigovariant-callingpcrindelscrispr-cas9sanger-chromatograms+ 6

  JavaScript

  •

  GNU General Public License v3.0

  •1010 forks•3636 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• bgen

  Public
  Barcode Generator

  genomicsdnahigh-throughput-sequencing+ 4

  genomicsdnahigh-throughput-sequencingdna-sequencesdna-sequencingdna-barcodegear-genomics

  JavaScript

  •

  GNU General Public License v3.0

  •22 forks•33 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• bistro

  Public
  bistro: barcode distribution

  genomicssequencingdna+ 2

  genomicssequencingdnadna-barcodegear-genomics

  HTML

  •

  GNU General Public License v3.0

  •22 forks•22 stars•00 issues•00 pull requests•Updated Dec 29, 2025Dec 29, 2025

• maze

  Public
  maze: match visualizer | visually align dna sequences using exact matches

  JavaScript

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 28, 2025Dec 28, 2025

• libs

  Public
  The libraries and fonts commonly used in the gear applications

  CSS

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 7, 2023Aug 7, 2023

• salt

  Public
  Sequence Alignment Tool

  dnaalignmentdna-sequences+ 2

  dnaalignmentdna-sequencespairwise-alignmentgear-genomics

  JavaScript

  •

  Other

  •1616 forks•00 stars•00 issues•00 pull requests•Updated Aug 3, 2023Aug 3, 2023

• verdin

  Public
  Variant Primer Design

  genomevariant-callingpcr+ 2

  genomevariant-callingpcrprimer-designgear-genomics

  Python

  •

  GNU General Public License v3.0

  •00 forks•33 stars•00 issues•00 pull requests•Updated Oct 11, 2021Oct 11, 2021

• primer3plus

  Public
  Primer3Plus is an advanced web interface for primer3.

  Perl

  •

  GNU General Public License v3.0

  •1111 forks•00 stars•00 issues•00 pull requests•Updated Oct 11, 2021Oct 11, 2021

• rdml-tools

  Public
  A collection of web applications to visualize, edit and validate RDML files.

  JavaScript

  •

  GNU General Public License v3.0

  •33 forks•00 stars•00 issues•00 pull requests•Updated Oct 11, 2021Oct 11, 2021