nf-core / rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Nextflow pipeline to call germline structural variants and copy number variants using DELLY and Manta
Repository to host tool-specific module files for the Nextflow DSL2 community!
Set of commonly used Nextflow modules
Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment
Nextflow pipeline to calculate read-depth related stats for targeted sequencing experiments
Nextflow pipeline to call germline short variants using GATK
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration