Nextflow Modules
Showing module(s) with keyword "contigs"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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/deeparg/predict | Process | deeparg antimicrobial resistance antimicrobial resistance genes arg deep learning prediction contigs metagenomes | A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes |
| nf-core/fargene | Process | antibiotic resistance genes ARGs identifier metagenomic contigs | tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. |
| nf-core/fasta_binning_concoct | Workflow | concoct binning metagenomics contigs | Runs the CONCOCT workflow of contig binning |
| nf-core/fasta_classify_catpack | Workflow | metagenomics taxonomy classification bins MAGs contigs CAT BAT | Taxonomic classification of binned MAGs and contigs using CAT/BAT (CAT_pack). |
| nf-core/gecco/run | Process | bgc detection metagenomics contigs | GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs). |
| nf-core/maxbin2 | Process |