Nextflow Modules
Showing module(s) with keyword "UMI"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_dedup_umi | Workflow | deduplication UMI BAM genome transcriptome umicollapse umitools | BAM deduplication with UMI processing for both genome and transcriptome alignments |
| nf-core/fastq_fastqc_umitools_fastp | Workflow | fastq fastqc qc UMI trimming fastp | Read QC, UMI extraction and trimming |
| nf-core/fastq_fastqc_umitools_trimgalore | Workflow | fastq fastqc qc UMI trimming trimgalore | Read QC, UMI extraction and trimming |
| 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/isoseq3/tag | Process | isoseq tag pacbio UMI cell_barcodes | Extract UMI and cell barcodes |
| nf-core/isoseq/tag | Process | isoseq tag pacbio UMI cell_barcodes | Extract UMI and cell barcodes |
| nf-core/umitools/extract | Process | UMI barcode extract umitools | Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place |