Nextflow Modules
Showing module(s) with keyword "scaffold"
| Module | Keywords | Description |
|---|---|---|
| nf-core/clusty | cluster network contig scaffold alignment protein | Clusty is a tool for large-scale clustering using sparse distance matrices, suitable for datasets with millions of objects. |
| 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/links | scaffold long-reads genomics | LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. This module is for LINKS >=2.0.0 and does not support MPET input. |
| nf-core/quast | quast assembly quality contig scaffold | Quality Assessment Tool for Genome Assemblies |
| 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. |