Nextflow Modules
Showing module(s) with keyword "virus"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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/cobrameta | Process | cobra contig scaffold assembly extension virus phage | A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly. |
| nf-core/genomad/download | Process | metagenomics genomad database download phage virus plasmid | Download geNomad databases and related files |
| nf-core/genomad/endtoend | Process | metagenomics genomad database download phage virus plasmid | Identify mobile genetic elements present in genomic assemblies |
| nf-core/phispy | Process | genomics virus phage prophage annotation identification | Predict prophages in bacterial genomes |
| nf-core/vclust/align | Process | cluster virus filter contig scaffold phage | The align command performs pairwise sequence alignments of viral genomes and provides similarity measures like ANI and coverage (alignment fraction) |
| nf-core/vclust/cluster | Process | cluster virus filter contig scaffold phage | Vclust cluster performs threshold-based clustering by assigning a genome sequence to a cluster if its similarity (e.g., ANI) to the cluster meets or exceeds a user-defined threshold. |
| nf-core/vclust/prefilter | Process | cluster virus filter contig scaffold phage | The prefilter command creates a pre-alignment filter that reduces the number of genome pairs to be aligned by filtering out dissimilar sequences before the alignment step. |
| nf-core/vcontact3/prepareddatabases | Process | virus database genomics clustering vcontact3 | Prepare and format databases for vCONTACT3 viral taxonomic analysis |
| nf-core/viralconsensus | Process | virus genomics consensus bam fasta | Fast and memory-efficient viral consensus genome sequence generation from read alignments |
| nf-core/virusrecom | Process | recombination virus genomics phylogenetics | Information-theory-based method for recombination detection of viral lineages using weighted information content (WIC). |
| nf-core/vrhyme/vrhyme | Process | binning bin phage virus vrhyme | Binning virus genomes from metagenomes |