Repositories list

• gens

  Public
  JavaScript

  •

  Mozilla Public License 2.0

  •5•12•33•2•Updated Nov 19, 2024Nov 19, 2024

• SomaticPanelPipeline

  Public
  Nextflow

  •2•0•16•2•Updated Nov 19, 2024Nov 19, 2024

• coyote_blueprinted

  Public
  Python

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• nextflow_wgs

  Public
  Perl

  •5•6•74•4•Updated Nov 18, 2024Nov 18, 2024

• jasentool

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•3•1•Updated Nov 15, 2024Nov 15, 2024

• bonsai

  Public
  Visualize and analyze resistance and outbreak of bacterial pathogen

  Standard ML

  •

  GNU General Public License v3.0

  •1•4•25•1•Updated Nov 15, 2024Nov 15, 2024

• coyote_cli

  Public
  command line interface for coyote

  Python

  •1•0•2•0•Updated Nov 15, 2024Nov 15, 2024

• PipeEval

  Public
  Evaluate changes to your pipelines.

  Python

  •

  Apache License 2.0

  •0•0•7•0•Updated Nov 14, 2024Nov 14, 2024

• bonsai-prp

  Public
  Pipeline output Processing Program for Bonsai

  Python

  •

  GNU General Public License v3.0

  •0•0•5•0•Updated Nov 11, 2024Nov 11, 2024

• gms_16S

  Public
  A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.

  Groovy

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• Pipeline-validation-tools

  Public
  Set of tools for assisting verifications and validations.

  Python

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• PGxModule

  Public
  PGxModule is an advanced Nextflow DSL2 workflow, designed to seamlessly integrate into your genomics pipeline. It empowers you to generate sample-specific reports with clinical guidelines, leveraging state-of-the-art variant detection in Genomic Medicine Sweden sequencing panels.

  Nextflow

  •

  GNU General Public License v3.0

  •0•1•6•0•Updated Nov 6, 2024Nov 6, 2024

• genmod

  Public
  Annotate models of genetic inheritance patterns in variant files (vcf files)

  Python

  •

  MIT License

  •19•0•0•0•Updated Oct 18, 2024Oct 18, 2024

• tomte

  Public
  Rare disease RNA sequencing pipeline based on nfcore

  Nextflow

  •

  MIT License

  •3•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• sc2reporter

  Public
  Perl

  •

  GNU General Public License v2.0

  •2•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• sc2-usher

  Public
  Scripts for creating sarscov2 usher trees, plus generating metadata including ECDC VOI/VUM

  Shell

  •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• nextflow_ST_rnaseqfus

  Public
  A rnaseq fussion detection assay at CMD

  Perl

  •0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

• qc_sentieon

  Public
  Script to generate json with relevant QC-data for WGS and panels

  Perl

  •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

• sarscov2-pipe

  Public
  A boring sars-cov-2 pipeline

  Shell

  •0•0•1•0•Updated Apr 26, 2024Apr 26, 2024

• cll_genie

  Public
  GNU General Public License v3.0

  •0•1•0•0•Updated Mar 18, 2024Mar 18, 2024

• skierfe

  Public
  Long read pipeline

  Nextflow

  •

  MIT License

  •4•0•0•0•Updated Feb 15, 2024Feb 15, 2024

• nextflow_tumwgs

  Public
  Perl

  •2•2•12•0•Updated Feb 2, 2024Feb 2, 2024

• Compare-VCF

  Public
  Compare and visualize VCF files and rank scores

  Python

  •0•0•2•0•Updated Jan 24, 2024Jan 24, 2024

• cmd_vcf

  Public
  python implementation of cmd vcf module

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 11, 2024Jan 11, 2024

• JASEN

  Public
  Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

  Nextflow

  •

  GNU General Public License v3.0

  •11•0•0•0•Updated Nov 16, 2023Nov 16, 2023

• pipeline_documentation

  Public
  This repo generates automatic documentation for pipelines or tools by using a pipeline.yaml file and producing both HTML and MD documents. The MD document can be uploaded to a readthedocs server for online documentation. It uses the mkdocs format, with the required "docs" folder and related files in the project root folder.

  Python

  •2•0•0•0•Updated Nov 6, 2023Nov 6, 2023

• Rank-Model-Validation-2023

  Public
  Python

  •0•0•0•0•Updated Nov 1, 2023Nov 1, 2023

• GrapeJuice

  Public
  GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html

  JavaScript

  •

  GNU General Public License v3.0

  •26•0•0•0•Updated Sep 29, 2023Sep 29, 2023

• nextflow_rnaseqfus

  Public
  Fusion genes identification pipeline

  Perl

  •4•1•8•2•Updated May 29, 2023May 29, 2023

• nextflow-modules

  Public
  Shared nextflow modules and assets

  Perl

  •

  GNU General Public License v3.0

  •2•0•0•1•Updated Apr 24, 2023Apr 24, 2023