Nextflow Modules
Showing module(s) with keyword "isoseq"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/gstama/collapse | Process | tama_collapse.py isoseq nanopore long-read transcriptome gene model TAMA | Collapse redundant transcript models in Iso-Seq data. |
| nf-core/gstama/merge | Process | gstama gstama/merge long-read isoseq nanopore tama trancriptome annotation | Merge multiple transcriptomes while maintaining source information. |
| nf-core/gstama/polyacleanup | Process | gstama gstama/polyacleanup long-read isoseq tama trancriptome annotation | Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3) |
| nf-core/isoseq3/tag | Process | isoseq tag pacbio UMI cell_barcodes | Extract UMI and cell barcodes |
| nf-core/isoseq/cluster | Process | cluster HiFi isoseq Pacbio | IsoSeq - Cluster - Cluster trimmed consensus sequences |
| nf-core/isoseq/cluster2 | Process | cluster HiFi isoseq Pacbio | IsoSeq - Cluster2 - Cluster full-length non-chimeric reads into transcripts |
| nf-core/isoseq/groupdedup | Process | dedup single-cell isoseq Pacbio | IsoSeq - GroupDedup - Deduplicate PCR artifacts grouped by cell barcode |
| nf-core/isoseq/refine | Process | isoseq refine ccs pacbio polyA_tail | Remove polyA tail and artificial concatemers |
| nf-core/isoseq/tag | Process | isoseq tag pacbio UMI cell_barcodes | Extract UMI and cell barcodes |
| nf-core/lima | Process | isoseq ccs primer pacbio barcode | lima - The PacBio Barcode Demultiplexer and Primer Remover |
| nf-core/pbccs | Process | ccs pacbio isoseq subreads | Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads |
| nf-core/ultra/align | Process | uLTRA align minimap2 long_read isoseq ont | uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome |
| nf-core/ultra/index | Process | uLTRA index minimap2 long_read isoseq ont | uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment |
| nf-core/ultra/pipeline | Process | uLTRA index minimap2 long_read isoseq ont | uLTRA aligner - A wrapper around minimap2 to improve small exon detection |