Stable
Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.
This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container
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Type: Common Workflow Language
Creators: Laura Rodriguez-Navas, José Mª Fernández
Submitter: Laura Rodriguez-Navas
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Work-in-progress
Workflow for read quality control and trimming.
Steps:
FastQC (read quality control)
fastp (read quality trimming)
bbduk used for rrna filtering
Work-in-progress
Type: Common Workflow Language
Creators: Stian Soiland-Reyes, Michael R. Crusoe, Pjotr Prins, Andrea Guarracino, Peter Amstutz, Thomas Liener, Adam Novak, Bonface Munyoki, Tazro Inutano Ohta, Michael Heuer
Submitter: Michael R. Crusoe
Stable
Analysis of variation within individual COVID-19 samples
using bowtie2, bwa, fastp, multiqc , picard ,samtools, snpEff
Workflow, tools and data are available on https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Variation
This worklow was ported into CWL from a Galaxy Workflow
( https://github.com/galaxyproject/SARS-CoV-2/tree/master/genomics/4-Variation migrated to CWL).
Stable
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using SAMTools.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Stable
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Stable
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using VARSCAN.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Stable
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
