binette
Description¶
Binette binning refinement tool
Keywords: mag, bins, refinement, metagenome, quality, checkm2, completeness, contamination
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install binette
Tools¶
binette¶
Binette: a fast and accurate bin refinement tool to construct high-quality Metagenome Assembled Genomes
- 10.21105/joss.06782
- GPL v3
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test' ] |
- |
input_binning |
file | One or multiple folders with FASTA files of each bin OR one or multiple TSV contig2bin tables, which establish the relationship between each contig and its corresponding bin. | *.{fasta,fna,fa,tsv} |
contigs |
file | A FASTA file containing all contigs that were used for binning. | *.{fasta,fna,fa} |
proteins |
file | A FASTA file containing predicted proteins from the contigs used for binning. Specify this input if you don't want Binette to predict proteins from the contigs. | *.{fasta,fna,fa} |
input_type |
string | Type of input binning format provided to Binette. Choose between fasta (for folders with bins FASTA files) or tsv (for TSV files that map contigs to bins). |
- |
checkm2_db |
file | CheckM2 database in Diamond format (.dmnd). Required for assessing bin quality and completeness. | *.dmnd |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
refined_bins |
file | - | |
refined_bins_report |
file | - | |
versions |
file | - |