Nextflow Modules
Showing module(s) with keyword "binning"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/binette | Process | binning refinement genomics metagenomics mag | A fast and accurate binning refinement tool to construct high quality MAGs from the output of multiple binning tools. |
| nf-core/clame | Process | sort genomics binning metagenomics | binning of metagenomic sequences |
| nf-core/comebin/runcomebin | Process | metagenomics binning clustering | Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning |
| nf-core/concoct/concoct | Process | 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/concoct/concoctcoveragetable | Process | contigs fragment mags binning bed bam subcontigs coverage | Generate the input coverage table for CONCOCT using a BEDFile |
| nf-core/concoct/cutupfasta | Process | contigs fragment mags binning fasta cut cut up | Cut up fasta file in non-overlapping or overlapping parts of equal length. |
| nf-core/concoct/extractfastabins | Process | contigs fragment mags binning fasta cut cut up bins merge | Creates a FASTA file for each new cluster assigned by CONCOCT |
| nf-core/concoct/mergecutupclustering | Process | contigs fragment mags binning fasta cut cut up merge | Merge consecutive parts of the original contigs original cut up by cut_up_fasta.py |
| nf-core/dastool/dastool | Process | binning das tool table de novo bins contigs assembly das_tool | DAS Tool binning step. |
| nf-core/dastool/fastatocontig2bin | Process | binning das tool table de novo bins contigs assembly das_tool | Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format |
| nf-core/dastool/scaffolds2bin | Process | binning das tool table de novo bins contigs assembly das_tool | Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format |
| nf-core/fairy/coverage | Process | metagenomics coverage binning alignment-free contig | Computes coverage depth statistics for assembled contigs from one or more fairy sketch files, producing a MetaBAT2-compatible TSV with per-contig mean depth and variance columns. |
| nf-core/fasta_binning_concoct | Workflow | concoct binning metagenomics contigs | Runs the CONCOCT workflow of contig binning |
| nf-core/maxbin2 | Process | metagenomics assembly binning maxbin2 de novo assembly mags metagenome-assembled genomes contigs | MaxBin is a software that is capable of clustering metagenomic contigs |
| nf-core/metabat2/jgisummarizebamcontigdepths | Process | sort binning depth bam coverage de novo assembly | Depth computation per contig step of metabat2 |
| nf-core/metabat2/metabat2 | Process | sort binning depth bam coverage de novo assembly | Metagenome binning of contigs |
| nf-core/metator/pipeline | Process | hic binning metagenomics | Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets. |
| nf-core/semibin/concatenatefasta | Process | concatenate fasta binning | Concatenate multiple sample FASTAs to a single FASTA with the correct header format for SemiBin2 |
| nf-core/semibin/multieasybin | Process | binning assembly-binning metagenomics | metagenomic binning with self-supervised learning |
| nf-core/semibin/singleeasybin | Process | binning assembly-binning metagenomics | metagenomic binning with self-supervised learning |