|
None |
3 |
Genomic Epidemiology of SARS-CoV-2 in Pakistan |
Apr 12, 2022 |
|
Perl |
12 |
Bioinformatics analysis of SARS-CoV-2 |
Apr 04, 2022 |
|
Python |
13 |
Daily analyses of genomic SARS-CoV-2 data |
Jun 07, 2022 |
|
Shell |
7 |
BEAR: viral diagnostic analysis pipeline for SARS-CoV-2 |
Jul 13, 2022 |
|
None |
2 |
SARS-CoV-2 resources for sequencing and genomic analysis |
Dec 09, 2021 |
|
R |
3 |
Phylogeographical analyses of SARS-CoV-2 variants of concern in Norway |
Jul 22, 2022 |
|
Python |
12 |
Identify Variants of Concern from metagenomic samples of SARS-CoV-2 |
Apr 05, 2023 |
|
None |
6 |
Models of SARS-CoV-2 genomic elements generated by FARFAR2 |
Oct 12, 2022 |
|
Nextflow |
20 |
Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub |
Jul 15, 2022 |
|
R |
2 |
Code for the paper Recent trends in SARS-CoV-2 variants of concern in England |
May 21, 2021 |
|
Jupyter Notebook |
2 |
Procedure used fro the surveillance of SARS-CoV-2 genomic variants in wastewater. |
Nov 30, 2021 |
|
Shell |
10 |
Curated datasets on reported cases of the SARS-CoV-2 Omicron (B.1.1.529) Variant of Concern |
Aug 03, 2022 |
|
HTML |
8 |
Data and files from the May 25, 2021 SARS-CoV-2 viral load and infectiousness paper |
Jan 20, 2022 |
|
Jupyter Notebook |
8 |
This is a repository for development of the SARS-CoV-2 Bioinformatics for Beginners Course |
Mar 02, 2023 |
|
Python |
2 |
mappgene (Massively Parallel and Portable Genomic Sequence Analysis) runs SARS-CoV-2 sequencing on HPC platforms. |
Feb 23, 2022 |
|
Nextflow |
4 |
An SARS-CoV-2 bioinformatics pipeline for CLIA validation using Dr. Erin Young's Cecret StaphB pipeline as … |
Jan 20, 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 |
4 |
None |
Mar 07, 2023 |
|
wdl |
38 |
Cloud-based scalable and efficient single-cell genomics workflows |
Dec 14, 2022 |
|
wdl |
2 |
A Cromwell workflow to call and filter variants from sequencing data. |
Mar 28, 2022 |
|
wdl |
5 |
Abraham's lab - ChipSeq Pipeline |
Feb 24, 2023 |
cromwell-output-reorganization
|
wdl |
2 |
None |
Apr 26, 2022 |
|
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 |
2 |
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools |
Jul 19, 2022 |
|
wdl |
2 |
Workflows for converting between sequence data formats |
Jul 19, 2022 |
|
wdl |
2 |
Subroutines of WARP for germline exome calling |
Jul 20, 2022 |
|
wdl |
2 |
Cromwell integration testing environment |
Dec 11, 2020 |
|
wdl |
2 |
Autogenerated WDLs for GATK Tools |
Jan 05, 2022 |
|
wdl |
2 |
Sample dockstore whalesay repo for testing |
Nov 22, 2021 |
|
wdl |
2 |
Pipeline Workflows |
Oct 20, 2019 |
topmed-workflow-variant-calling
|
wdl |
2 |
None |
Jun 20, 2020 |
|
wdl |
3 |
Workflows used for processing whole genome sequence data + germline variant calling. |
Jul 19, 2022 |
|
wdl |
3 |
Workflows to run ADAPT on AWS Batch. |
Mar 03, 2022 |