fastq_create_umi_consensus_fgbio
This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads convert them to unmapped BAM file, map them to the reference genome, and finally use the mapped information to group UMIs and generate consensus reads in each group
Description
This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads convert them to unmapped BAM file, map them to the reference genome, and finally use the mapped information to group UMIs and generate consensus reads in each group
Input
A read structure should always be provided for each of the fastq files.
If single end, the string will contain only one structure (i.e. โ2M11S+Tโ), if paired-end the string
will contain two structures separated by a blank space (i.e. โ2M11S+T 2M11S+Tโ).
If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).
https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
