A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using ‘N’.
Creator: David F. Nieuwenhuijse, Alexey Sokolov
Submitter: Ross Thorne
Workflow for NonSpliced RNAseq data with multiple aligners.
bowtie2 (read mapping)
featurecounts (transcript read counts)
kallisto (transcript [pseudo]counts)
Workflow to build different indices for different tools from a genome and transcriptome.
This workflow expects an (annotated) genome in GBOL ttl format.
SAPP: rdf2gtf (genome fasta)
SAPP: rdf2fasta (transcripts fasta)
STAR index (Optional for Eukaryotic origin)
Type: Common Workflow Language
Submitter: Bart Nijsse