Repositories list

• EM-seq

  Public
  Tools and Data related to Enzymatic Methylation Sequencing

  Nextflow

  •

  GNU Affero General Public License v3.0

  •5•16•5•1•Updated Dec 17, 2024Dec 17, 2024

• fatools

  Public
  A Python library for performing DNA fragment-analysis

  Python

  •

  GNU Lesser General Public License v3.0

  •12•0•1•0•Updated Dec 17, 2024Dec 17, 2024

• domainator

  Public
  A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.

  Python

  •

  Other

  •1•15•14•0•Updated Dec 16, 2024Dec 16, 2024

• tasmanian-mismatch

  Public
  Analysis of artifacts in high throughput sequencing data from genomic DNA.

  HTML

  •

  Other

  •0•1•8•3•Updated Dec 3, 2024Dec 3, 2024

• 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 17, 2024Nov 17, 2024

• 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•3•3•8•Updated Nov 3, 2024Nov 3, 2024

• 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

• iwc

  Public
  Intergalactic Workflow Commission

  Python

  •73•0•0•0•Updated Jun 29, 2024Jun 29, 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

• plate-map

  Public
  A flexible tool for defining the contents of 96 well plates.

  JavaScript

  •

  GNU Affero General Public License v3.0

  •13•47•7•5•Updated Jun 20, 2024Jun 20, 2024

• rsvAB-sequencing

  Public
  NEBNext RSV A/B Multiplex PCR sequencing primers

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Jun 3, 2024Jun 3, 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. 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.

  sequencingpcrtargeted-sequencing+ 1sars-cov-2

  Rust

  •

  GNU Affero General Public License v3.0

  •1•14•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

• 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•6•0•Updated Aug 15, 2023Aug 15, 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 failed bit to prevent these reads from being used in downstream methylation calling. It also prints summary information to stderr.

  Python

  •

  GNU Affero General Public License v3.0

  •1•3•3•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

  •630•0•0•0•Updated Feb 6, 2023Feb 6, 2023

• seq-results-deprecated

  Public
  Deprecated: Web interface to manage a database of sequence results (merged into ngs-aggregate-results)

  Ruby

  •

  GNU Affero General Public License v3.0

  •0•1•2•9•Updated Dec 14, 2022Dec 14, 2022

• poreCov

  Public
  SARS-CoV-2 workflow for nanopore sequence data

  Nextflow

  •

  GNU General Public License v3.0

  •17•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

  •53•0•0•0•Updated Jul 11, 2022Jul 11, 2022

• VarSkip

  Public
  VarSkip multiplex PCR designs for SARS-CoV-2 sequencing

  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

  •19•0•0•0•Updated Jun 10, 2022Jun 10, 2022

• artic-ncov2019

  Public
  ARTIC nanopore protocol for nCoV2019 novel coronavirus

  Python

  •

  Creative Commons Attribution 4.0 International

  •165•0•0•0•Updated Aug 16, 2021Aug 16, 2021

• Cas-PAM-cleavage-analysis

  Public
  Shell

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Aug 6, 2021Aug 6, 2021

• primer-schemes

  Public
  Primer schemes for real-time genome epidemiology

  Python

  •

  Creative Commons Attribution 4.0 International

  •42•0•0•0•Updated Jul 10, 2021Jul 10, 2021

• ngslite

  Public
  Light-weight functions for next-generation sequencing (NGS) data analysis

  Python

  •

  MIT License

  •1•0•0•0•Updated Jun 15, 2021Jun 15, 2021