|
|
wdl |
2 |
Workflows used for germline short variant discovery in WGS data - replaced by https://github.com/microsoft/gatk4-genome-processing-pipeline-azure |
Jul 19, 2022 |
|
|
wdl |
51 |
Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad … |
Mar 24, 2023 |
|
|
wdl |
3 |
Workflows used for processing whole genome sequence data + germline variant calling. |
Jul 19, 2022 |
|
|
Shell |
2 |
Viral genome assembly pipeline for WGS using ONT |
Jan 27, 2023 |
|
|
Python |
2 |
Pipeline for processing whole-genome Population STARR-seq data |
May 28, 2021 |
|
|
Shell |
11 |
BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA |
Mar 10, 2023 |
|
|
wdl |
2 |
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools |
Jul 19, 2022 |
|
|
wdl |
127 |
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools |
Mar 29, 2023 |
|
|
Java |
34 |
Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead |
Nov 19, 2019 |
|
|
Python |
2 |
Snakemake Pipeline for processing BioMob WP2 partial genome sequencing data |
Jun 29, 2023 |
|
|
Groovy |
6 |
A bpipe pipeline for processing WGS from Plasmodium facliparum |
Aug 08, 2022 |
|
|
Shell |
2 |
Nextflow script for processing WGS data |
Aug 28, 2023 |
|
|
Scala |
3 |
GATK QScripts used in our illumina variant calling pipeline. |
Jul 22, 2016 |
|
|
wdl |
48 |
Workflows for processing RNA data for germline short variant discovery with GATK v4 and related … |
Apr 26, 2023 |
|
|
wdl |
46 |
Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related … |
Apr 14, 2023 |
|
|
Python |
105 |
Processing pipeline for pan-genome visulization and exploration |
Aug 19, 2022 |
|
|
Python |
4 |
Import data into MongoDB for use by https://github.com/genome-nexus/genome-nexus/ |
Apr 11, 2023 |
|
|
AGS Script |
3 |
Workflows used for morphology processing. |
Aug 12, 2022 |
|
|
Ruby |
584 |
Replaced by https://github.com/github/scientist |
Dec 19, 2021 |
|
|
Python |
5 |
Replaced by: https://github.com/chembl/tractability_pipeline_v2 |
Jan 28, 2023 |
|
|
TypeScript |
2 |
Replaced by https://github.com/theoparis/trippy |
Jan 28, 2023 |
|
|
wdl |
3 |
Workflow used for WGS/WES data QC |
Apr 20, 2023 |
|
|
M4 |
6 |
Deprecated; replaced by: https://github.com/UnixJunkie/cpu |
Dec 11, 2019 |
|
|
PHP |
9 |
replaced by https://github.com/catalyst/moodle-local_cohortauto |
Feb 01, 2022 |
|
|
Go |
3 |
Replaced with: https://github.com/iris-contrib/schema |
Jul 24, 2019 |
|
|
QML |
3 |
Replaced by https://github.com/ubports/morph-browser |
Nov 28, 2018 |
|
|
TypeScript |
6 |
Replaced by Repo: https://github.com/alvachien/knowledgebuilder |
Jan 28, 2023 |
|
|
JavaScript |
39 |
Replaced by https://github.com/tosdr/browser-extensions |
Jan 28, 2023 |
|
|
Nextflow |
2 |
Single Cell Genome Sequencing data analysis pipeline |
Nov 08, 2022 |
|
|
wdl |
4 |
Workflows for somatic short variant discovery with GATK4 |
Jul 19, 2022 |
|
|
wdl |
4 |
Repo For the WDL Testathon held February 18 - 19, 2020 |
Mar 20, 2020 |
|
|
wdl |
4 |
ENCODE DNase-seq pipeline |
Feb 28, 2021 |
|
|
wdl |
6 |
A coot trans flag using GitHub language colors! |
Apr 19, 2022 |
pb-human-wgs-workflow-wdl
|
wdl |
6 |
None |
Jul 25, 2022 |
|
|
wdl |
7 |
bioinformatics pipelines |
Mar 10, 2022 |
|
|
wdl |
7 |
This is primarily a repo for capturing policies and discussions around the different workflows for … |
Jan 31, 2022 |
|
|
wdl |
8 |
None |
Jul 14, 2022 |
|
|
wdl |
10 |
Utility workflows for the DSP hydro.gen team (formerly palantir) |
Apr 03, 2022 |
|
|
wdl |
10 |
a place for topmed workflows |
Feb 03, 2022 |
|
|
wdl |
12 |
None |
May 27, 2022 |
|
|
wdl |
2 |
A Dockstore WDL Workflow that uses UShER to place your consensus.fasta sequences on the SARS-CoV-2 … |
Nov 13, 2021 |
|
|
wdl |
2 |
WDL workflows to build genetic maps from sequencing reads |
Mar 16, 2023 |
|
|
wdl |
2 |
Metagenome Annotation Workflow |
Apr 25, 2023 |
|
|
wdl |
2 |
None |
Apr 25, 2023 |
|
|
wdl |
13 |
Evaluating genome assemblies |
Apr 18, 2023 |
public_health_bacterial_genomics
|
wdl |
24 |
None |
Mar 14, 2023 |
public_health_bioinformatics
|
wdl |
6 |
None |
Apr 17, 2023 |
|
|
wdl |
30 |
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, … |
Dec 14, 2022 |
|
|
wdl |
4 |
None |
Mar 07, 2023 |
|
|
wdl |
38 |
Cloud-based scalable and efficient single-cell genomics workflows |
Dec 14, 2022 |