Nextflow Modules
Showing module(s) with keyword "microbiome"
| 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/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 metagenomics contamination removal microbiome | Builds a Cuckoo filter or Cuckoo hash table index from reference sequences (FASTA/FASTQ) for fast contamination removal. |
| nf-core/grimer | Process | 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/malt/build | Process | malt alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome database | MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. |
| nf-core/maltextract | Process | malt MaltExtract HOPS alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome authentication damage edit distance | Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening |
| nf-core/malt/run | Process | malt alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome | MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. |
| nf-core/picrust2/pipeline | Process | metagenomics functional prediction 16S microbiome | Predict metagenome functional content from marker gene sequences and OTU/ASV abundance data |
| nf-core/vsearch/cluster | Process | vsearch clustering microbiome | Cluster sequences using a single-pass, greedy centroid-based clustering algorithm. |