Nextflow Modules
Showing module(s) with keyword "deduplication"
| Module | Keywords | Description |
|---|---|---|
| nf-core/custom/orfcollapse | orf ribo-seq catalogue smorf deduplication | Collapse small ORFs that share an amino-acid sequence cluster into a single catalogue entry. Pair with `custom/orfmerge` (coordinate-based catalogue), `bedtools/getfasta` + `seqkit/translate` (AA FASTA keyed by orf_id), and `mmseqs/easycluster` (AA clusters) upstream. The coordinate-based merge in `custom/orfmerge` only groups ORFs that overlap on the genome, so the same micropeptide encoded at several distinct, non-overlapping loci (typically repetitive regions) survives as separate rows. This adopts the peptide-level deduplication and 0.9 amino-acid-similarity threshold of the GENCODE Ribo-seq ORF consolidation (Mudge et al. 2022, Nat Biotechnol, doi:10.1038/s41587-022-01369-0; gencode-riboseqORFs collapse_cutoff 0.9), implemented here with MMseqs2 sequence-identity clustering rather than that tool's longest-shared-string / P-site-overlap metric. Small ORFs (`aa_length` <= `--smorf-max-aa`, default 100) are clustered by amino-acid identity upstream and this module folds each multi-member cluster down to one representative. Only small ORFs are collapsed; larger ORFs are passed through untouched. Eligibility is the catalogue's `is_smorf` flag, independent of `orf_class`, so a short uORF and a short novel ORF are both candidates; `--smorf-max-aa` re-derives the flag and aborts on disagreement. Among the members of a cluster the representative is chosen by class specificity, then longest aa_length, then orf_id, so the result does not depend on which sequence MMseqs2 labelled the cluster representative. Catalogue row order is preserved; dropped members fold their `called_by_<caller>` / `score_<caller>` evidence, `n_samples` / `samples` recurrence and gene mappings into the survivor. |
| nf-core/dedup | dedup deduplication pcr duplicates ancient DNA paired-end bam | DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). |
| nf-core/fgumi/dedup | UMIs deduplication duplicates bam | Mark or remove PCR duplicates using UMI information with fgumi |
| nf-core/humid | umi fastq deduplication hamming-distance clustering | HUMID is a tool to quickly and easily remove duplicate reads from FASTQ files, with or without UMIs. |
| nf-core/pairtools/dedup | dedup deduplication PCR/optical duplicates pairs | Find and remove PCR/optical duplicates |
| nf-core/umicollapse | umicollapse deduplication genomics | Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. |
| nf-core/umitools/dedup | umitools deduplication dedup | Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. |
| nf-core/umitools/group | umitools umi deduplication dedup clustering | Group reads based on their UMI and mapping coordinates |