Nextflow Modules
Showing module(s) with keyword "deduplication"
| 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/custom/orfcollapse | Process | 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 | Process | 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/fastq_shortreads_preprocess_qc | Workflow | fastq illumina short reads qc stats preprocessing barcoding adapters merge complexity deduplication host decontamination | Quality check and preprocessing subworkflow of Illumina short reads that can do: quality check of input reads and generate statistics, preprocess and validate reads, barcode removal, remove adapters and merge reads, filter by sequence complexity, deduplicate reads, remove host contamination, concatenate reads and generate statistics for post-processing reads. WARNING: requires at least the process configurations from the nextflow.config to be added to the modules.config in the pipeline in order to work as intended. |
| nf-core/fgumi/dedup | Process | UMIs deduplication duplicates bam | Mark or remove PCR duplicates using UMI information with fgumi |
| nf-core/humid | Process | 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 | Process | dedup deduplication PCR/optical duplicates pairs | Find and remove PCR/optical duplicates |
| nf-core/umicollapse | Process | umicollapse deduplication genomics | Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. |
| nf-core/umitools/dedup | Process | umitools deduplication dedup | Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. |
| nf-core/umitools/group | Process | umitools umi deduplication dedup clustering | Group reads based on their UMI and mapping coordinates |