Nextflow Modules
Showing module(s) with keyword "metagenomics"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/amps | Process | malt MaltExtract HOPS amps alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome authentication damage edit distance post Post-processing visualisation | Post-processing script of the MaltExtract component of the HOPS package |
| nf-core/argnorm | Process | amr antimicrobial resistance arg antimicrobial resistance genes genomics metagenomics normalization drug categorization | Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD). |
| nf-core/binette | Process | binning refinement genomics metagenomics mag | A fast and accurate binning refinement tool to construct high quality MAGs from the output of multiple binning tools. |
| nf-core/biomformat/convert | Process | biom feature table formatting conversion amplicon sequences metagenomics metatranscriptomics | Convert biom table to different format. Conversion between text tab-delimited, BIOM-v1 (JSON), and BIOM-v2 (HDF5) formats are supported |
| nf-core/bracken/bracken | Process | bracken metagenomics abundance kraken2 | Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken. |
| nf-core/bracken/combinebrackenoutputs | Process | bracken metagenomics postprocessing reporting | Combine output of metagenomic samples analyzed by bracken. |
| nf-core/centrifuge/build | Process | database metagenomics build db fasta | Build centrifuge database for taxonomic profiling |
| nf-core/centrifuge/centrifuge | Process | classify metagenomics fastq db | Classifies metagenomic sequence data |
| nf-core/centrifuge/kreport | Process | classify metagenomics fastq db report kraken | Creates Kraken-style reports from centrifuge out files |
| nf-core/centrifuger/build | Process | metagenomics taxonomic-classification database-build centrifuger centrifuge | Build centrifuger database for taxonomic profiling |
| nf-core/centrifuger/centrifuger | Process | metagenomics classification centrifuger | Classification of sequencing reads using the Centrifuger tool. |
| nf-core/centrifuger/quantification | Process | metagenomics quantification Centrifuger | Quantification (taxonomic profiling) of Centrifuger model |
| nf-core/clame | Process | sort genomics binning metagenomics | binning of metagenomic sequences |
| nf-core/cleanifier/download | Process | download index metagenomics contamination removal microbiome | Download human reference index |
| nf-core/cleanifier/filter | Process | contamination removal metagenomics microbiome filter | Fast, lightweight contamination removal from microbiome data (FASTQ) using a probabilistic Cuckoo filter or Cuckoo hash table index |
| nf-core/cleanifier/index | Process | index genomics |