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    60 repositories

    • domainator

      Public
      A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.
      Python
      •
      Other
      •2•28•13•0•Updated Apr 25, 2026Apr 25, 2026

    • tasmanian-mismatch

      Public
      Analysis of artifacts in high throughput sequencing data from genomic DNA.
      HTML
      •
      Other
      •1•0•9•2•Updated Apr 24, 2026Apr 24, 2026

    • plate-map

      Public
      A flexible tool for defining the contents of 96 well plates.
      JavaScript
      •
      GNU Affero General Public License v3.0
      •15•52•7•0•Updated Apr 21, 2026Apr 21, 2026

    • bamslice

      Public
      slices a bam file into chunks of interleaved fastq for efficient downstream processing
      Rust
      •
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated Apr 21, 2026Apr 21, 2026

    • EM-seq

      Public
      Tools and Data related to Enzymatic Methylation Sequencing
      Nextflow
      •
      GNU Affero General Public License v3.0
      •8•34•8•2•Updated Apr 20, 2026Apr 20, 2026

    • EM-seq_variant_calling

      Public
      Nextflow
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • fatools

      Public
      A Python library for performing DNA fragment-analysis
      Python
      •
      GNU Lesser General Public License v3.0
      •12•0•1•0•Updated Feb 3, 2026Feb 3, 2026

    • mazf-cleavage

      Public
      MazF cleavage specificity data analysis
      HTML
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • rsvAB-sequencing

      Public
      NEBNext RSV A/B Multiplex PCR sequencing primers
      GNU Affero General Public License v3.0
      •1•1•0•0•Updated Nov 25, 2025Nov 25, 2025

    • low_bismap_methyl_calls

      Public
      Tools to assess called methylation in low mappability regions (as defined by bismap). Aligner MapQ does not always align with low mappability
      TeX
      •
      GNU Affero General Public License v3.0
      •0•0•4•0•Updated Nov 6, 2025Nov 6, 2025

    • NEBNextFluA

      Public
      Details and analysis recommendations for use with the NEBNext Flu A Integrated Indexing Primer Module (NEB #E3436S)
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • dna-polymerase-fidelity

      Public
      Computational pipeline to measure DNA polymerase fidelity (second strand DNA synthesis)
      Perl
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • iwc

      Public
      Intergalactic Workflow Commission
      Vue
      •90•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • primer_monitor

      Public
      a service to allow people to register primers to be monitored for intersecting variants and be notified if new variants arise
      Ruby
      •
      GNU Affero General Public License v3.0
      •3•4•3•9•Updated Mar 21, 2025Mar 21, 2025

    • uncleShiny

      Public
      A dashboard for Unchained Labs Uncle data visualization written in R using Shiny.
      R
      •
      GNU Affero General Public License v3.0
      •0•0•8•0•Updated Feb 26, 2025Feb 26, 2025

    • wps-ss-generator

      Public
      This is an attempt to streamline 96 well assembly / combination of ONT WPS submissions to the Sequencing Core
      JavaScript
      •0•1•0•0•Updated Sep 30, 2024Sep 30, 2024

    • domainator_examples

      Public
      Advanced examples of how to use the Domainator bioinformatics software suite
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • FFPE_nextflow_workflow

      Public
      Workflow to analyze FFPE ngs data
      Nextflow
      •
      GNU Affero General Public License v3.0
      •0•0•0•1•Updated Jun 28, 2024Jun 28, 2024

    • iiMS_InfluenzaA

      Public
      NEBNext iiMS Influenza A Library Prep for ONT
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated Jun 3, 2024Jun 3, 2024

    • ampseer

      Public
      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. …
      sequencingpcrtargeted-sequencing
      sequencingpcrtargeted-sequencingsars-cov-2
      Rust
      •
      GNU Affero General Public License v3.0
      •1•15•5•0•Updated Feb 27, 2024Feb 27, 2024

    • unclePy

      Public
      A parser for Unchained Labs Uncle HDF5 binary files written in Python.
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•4•0•Updated Sep 21, 2023Sep 21, 2023

    • opentrons

      Public
      Collection of scripts which can be used in relation to Opentrons OT-2 Liquid Handling Robot
      Python
      •1•0•0•0•Updated Aug 3, 2023Aug 3, 2023

    • mark-nonconverted-reads

      Public
      This program examines a BAM or SAM stream for reads that contain multiple Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and sets the vendor …
      Python
      •
      GNU Affero General Public License v3.0
      •1•3•4•0•Updated May 16, 2023May 16, 2023

    • picard_bcl_to_fastq

      Public
      Demultiplexes a MiSeq, NextSeq or HiSeq run using Picard's IlluminaBasecallsToFastq
      Nextflow
      •1•1•0•0•Updated Mar 28, 2023Mar 28, 2023

    • formtastic

      Public
      A Rails form builder plugin with semantically rich and accessible markup.
      Ruby
      •
      MIT License
      •624•0•0•0•Updated Feb 6, 2023Feb 6, 2023

    • poreCov

      Public
      SARS-CoV-2 workflow for nanopore sequence data
      Nextflow
      •
      GNU General Public License v3.0
      •18•0•0•0•Updated Aug 23, 2022Aug 23, 2022

    • neb-galaxy-workflows

      Public
      Galaxy Workflows
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Jul 19, 2022Jul 19, 2022

    • usegalaxy-tools

      Public
      usegalaxy.* common tools
      Shell
      •67•0•0•0•Updated Jul 11, 2022Jul 11, 2022

    • VarSkip

      Public
      VarSkip multiplex PCR designs for SARS-CoV-2 sequencing
      sequencingpcrsars-cov-2
      sequencingpcrsars-cov-2
      GNU Affero General Public License v3.0
      •9•14•0•0•Updated Jun 14, 2022Jun 14, 2022

    • datasets-sars-cov-2

      Public
      Perl
      •
      Apache License 2.0
      •25•0•0•0•Updated Jun 10, 2022Jun 10, 2022
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