Nextflow Modules
Showing module(s) with keyword "contamination"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/authentict/deam2cont | Process | authentict ancientDNA single-stranded deamination contamination damage | Use deamination patterns to estimate contamination in single-stranded libraries |
| 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/bam_docounts_contamination_angsd | Workflow | angsd bam contamination docounts | Calculate contamination of the X-chromosome with ANGSD |
| nf-core/checkm2/databasedownload | Process | checkm mag metagenome quality completeness contamination bins | CheckM2 database download |
| nf-core/checkm2/predict | Process | checkm mag metagenome quality completeness contamination bins | CheckM2 bin quality prediction |
| nf-core/checkm/lineagewf | Process | checkm mag metagenome quality isolates microbes single cells completeness contamination bins genome bins | CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. |
| nf-core/checkm/qa | Process | checkm mag metagenome quality isolates microbes single cells completeness contamination bins genome bins qa quality assurnce | CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. |
| nf-core/checkv/downloaddatabase | Process | checkv checkm mag metagenome quality isolates virus completeness contamination download database | Construct the database necessary for checkv's quality assessment |
| nf-core/checkv/endtoend | Process | checkv checkm mag metagenome quality isolates virus completeness contamination | Assess the quality of metagenome-assembled viral genomes. |
| nf-core/checkv/updatedatabase | Process | checkv checkm mag metagenome quality isolates virus completeness contamination | Construct the database necessary for checkv's quality assessment |
| nf-core/fastq_align_bamcmp_bwa | Workflow | bam cram bamcmp contamination align | Align reads to two different reference genomes using bwa, then use bamcmp to keep only reads that align better to the first genome, then sort with samtools |
| nf-core/fastq_contam_seqtk_kraken | Workflow | statistics fastq contamination | Produces a contamination report from FastQ input after subsampling |
| nf-core/fcs/fcsadaptor | Process | assembly genomics quality control contamination |