Nextflow Modules
Showing module(s) with keyword "xenograft"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bamcmp | Process | filter xenograft host graft contamination mouse | Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX). |
| nf-core/disambiguate | Process | disambiguation xenograft explant rna-seq alignment bam | Disambiguates reads aligned to two different organisms (e.g. human and mouse) from the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows where reads from two species are present. For reads aligned to both organisms, the algorithm compares alignment quality scores to determine the most likely species of origin. Produces four BAM files (uniquely assigned to species A or B, ambiguous for species A or B) and a summary file. |
| nf-core/xengsort/classify | Process | classify sort xenograft fastq cuckoo hash k-mer | Classify and sort FASTQ reads into host, graft, both, neither, or ambiguous categories using a xengsort hash index. |
| nf-core/xengsort/index | Process | index xenograft sorting cuckoo hash k-mer host graft | Build a bucketed 3-way Cuckoo hash table index from host and graft reference FASTA files for xenograft read sorting. |