Nextflow Modules
Showing module(s) with keyword "metagenomics"
| Module | Keywords | Description |
|---|---|---|
| nf-core/amps | 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 | 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/biomformat/convert | 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 | bracken metagenomics abundance kraken2 | Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken. |
| nf-core/bracken/combinebrackenoutputs | bracken metagenomics postprocessing reporting | Combine output of metagenomic samples analyzed by bracken. |
| nf-core/centrifuge/build | database metagenomics build db fasta | Build centrifuge database for taxonomic profiling |
| nf-core/centrifuge/centrifuge | classify metagenomics fastq db | Classifies metagenomic sequence data |
| nf-core/centrifuge/kreport | classify metagenomics fastq db report kraken | Creates Kraken-style reports from centrifuge out files |
| nf-core/centrifuger/build | metagenomics taxonomic-classification database-build centrifuger centrifuge | Build centrifuger database for taxonomic profiling |
| nf-core/centrifuger/centrifuger | metagenomics classification centrifuger | Classification of sequencing reads using the Centrifuger tool. |
| nf-core/centrifuger/quantification | metagenomics quantification Centrifuger | Quantification (taxonomic profiling) of Centrifuger model |
| nf-core/clame | sort genomics binning metagenomics | binning of metagenomic sequences |
| nf-core/cleanifier/download | download index metagenomics contamination removal microbiome | Download human reference index |
| nf-core/cleanifier/filter | 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 | index genomics metagenomics contamination removal microbiome | Builds a Cuckoo filter or Cuckoo hash table index from reference sequences (FASTA/FASTQ) for fast contamination removal. |
| nf-core/comebin/runcomebin | metagenomics binning clustering | Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning |
| nf-core/concoct/concoct | contigs fragment mags binning concoct kmer nucleotide composition metagenomics bins | Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples |
| nf-core/conifer | classify metagenomics kraken2 confidence | Calculate confidence scores from Kraken2 output |
| nf-core/coverm/contig | mapping genomics metagenomics coverage | Map reads to contigs and estimate coverage |
| nf-core/coverm/genome | mapping genomics metagenomics coverage | Calculate read coverage per-genome |