Nextflow Modules
Showing module(s) with keyword "contamination"
| Module | Keywords | Description |
|---|---|---|
| nf-core/authentict/deam2cont | authentict ancientDNA single-stranded deamination contamination damage | Use deamination patterns to estimate contamination in single-stranded libraries |
| nf-core/bamcmp | 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/checkm2/databasedownload | checkm mag metagenome quality completeness contamination bins | CheckM2 database download |
| nf-core/checkm2/predict | checkm mag metagenome quality completeness contamination bins | CheckM2 bin quality prediction |
| nf-core/checkm/lineagewf | 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 | 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 | checkv checkm mag metagenome quality isolates virus completeness contamination download database | Construct the database necessary for checkv's quality assessment |
| nf-core/checkv/endtoend | checkv checkm mag metagenome quality isolates virus completeness contamination | Assess the quality of metagenome-assembled viral genomes. |
| nf-core/checkv/updatedatabase | checkv checkm mag metagenome quality isolates virus completeness contamination | Construct the database necessary for checkv's quality assessment |
| nf-core/fcs/fcsadaptor | assembly genomics quality control contamination NCBI | Run NCBI's FCS adaptor on assembled genomes |
| nf-core/fcs/fcsgx | assembly genomics quality control contamination NCBI | Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid. |
| nf-core/fcsgx/cleangenome | genome assembly contamination screening cleaning fcs-gx | Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies |
| nf-core/fcsgx/rungx | genome assembly contamination screening cleaning fcs-gx | Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies |
| nf-core/grimer | metagenomics contamination visualisation taxonomy viromics microbiome dashboard | Generates an interactive HTML dashboard integrating taxonomy, annotation, and metadata to detect contamination in metagenomic and amplicon sequencing datasets. GRIMER is independent of quantification methods and directly analyses contingency tables. |
| nf-core/haplocheck | mitochondrial mtDNA contamination | Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides users a graphical report to investigate the contamination further. Internally, it uses the Haplogrep tool, that supports rCRS and RSRS mitochondrial versions. |
| nf-core/mash/screen | screen containment contamination taxonomic assignment | Screens query sequences against large sequence databases |
| nf-core/ncbitools/vecscreen | assembly genomics quality control contamination vector NCBI | NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose |
| nf-core/verifybamid/verifybamid | qc contamination bam | Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis. |
| nf-core/verifybamid/verifybamid2 | contamination bam verifybamid DNA contamination estimation | Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis. |