Nextflow Modules
Showing module(s) with keyword "virus"
| Module | Keywords | Description |
|---|---|---|
| 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/cobrameta | 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 | metagenomics genomad database download phage virus plasmid | Download geNomad databases and related files |
| nf-core/genomad/endtoend | metagenomics genomad database download phage virus plasmid | Identify mobile genetic elements present in genomic assemblies |
| nf-core/phispy | genomics virus phage prophage annotation identification | Predict prophages in bacterial genomes |
| nf-core/vclust/align | 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 | 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 | 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/viralconsensus | virus genomics consensus bam fasta | Fast and memory-efficient viral consensus genome sequence generation from read alignments |
| nf-core/vrhyme/vrhyme | binning bin phage virus vrhyme | Binning virus genomes from metagenomes |