Nextflow Modules
Showing module(s) with keyword "fgbio"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/fastq_create_umi_consensus_fgbio | Workflow | fgbio umi samblaster samtools bwa | 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 |
| nf-core/fgbio/callduplexconsensusreads | Process | umi duplex fgbio | Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule. |
| nf-core/fgbio/copyumifromreadname | Process | fgbio copy umi readname | Copies the UMI at the end of a bam files read name to the RX tag. |
| nf-core/fgbio/filterconsensusreads | Process | fgbio filter consensus umi duplexumi | Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. |
| nf-core/fgbio/groupreadsbyumi | Process | UMI groupreads fgbio | Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5’ mapping positions of the reads from the template, used from earliest mapping position to latest. Reads that have the same end positions are then sub-grouped by UMI sequence. (!) Note: the MQ tag is required on reads with mapped mates (!) This can be added using samblaster with the optional argument --addMateTags. |
| nf-core/fgbio/zipperbams | Process | fgbio umi unmapped ubam zipperbams | FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM |