Nextflow Modules
Showing module(s) with keyword "host"
| 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/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/iphop/download | Process | metagenomics iphop database download phage bacteria host | Download, extract, and check md5 of iPHoP databases |
| nf-core/iphop/predict | Process | metagenomics iphop database download phage bacteria host | Predict phage host using iPHoP |
| 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. |