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    56 repositories

    • EM-seq

      Public
      Tools and Data related to Enzymatic Methylation Sequencing
      Nextflow
      •
      GNU Affero General Public License v3.0
      •5•16•5•1•Updated Oct 20, 2024Oct 20, 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 Oct 9, 2024Oct 9, 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

    • 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 Sep 27, 2024Sep 27, 2024

    • tasmanian-mismatch

      Public
      Analysis of artifacts in high throughput sequencing data from genomic DNA.
      HTML
      •
      Other
      •0•1•7•3•Updated Sep 25, 2024Sep 25, 2024

    • domainator

      Public
      A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.
      Python
      •
      Other
      •1•13•14•0•Updated Sep 10, 2024Sep 10, 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
      •64•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•1•0•0•Updated Jun 3, 2024Jun 3, 2024

    • fatools

      Public
      A Python library for performing DNA fragment-analysis
      Python
      •
      GNU Lesser General Public License v3.0
      •12•0•1•0•Updated May 31, 2024May 31, 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-sequencingsars-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
      •628•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
      •52•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•13•0•0•Updated Jun 14, 2022Jun 14, 2022

    • datasets-sars-cov-2

      Public
      Perl
      •
      Apache License 2.0
      •18•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
      •41•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