name: maxbin2 description: MaxBin is a software that is capable of clustering metagenomic contigs keywords: - metagenomics - assembly - binning - maxbin2 - de novo assembly - mags - metagenome-assembled genomes - contigs tools: - maxbin2: description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. homepage: https://sourceforge.net/projects/maxbin/ documentation: https://sourceforge.net/projects/maxbin/ tool_dev_url: https://sourceforge.net/projects/maxbin/ doi: "10.1093/bioinformatics/btv638" licence: ['BSD 3-clause'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - contigs: type: file description: Multi FASTA file containing assembled contigs of a given sample pattern: "*.fasta" - reads: type: file description: Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files. pattern: "*.fasta" - abund: type: file description: Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files. output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - binned_fastas: type: file description: Binned contigs, one per bin designated with numeric IDs pattern: "*.fasta.gz" - summary: type: file description: Summary file describing which contigs are being classified into which bin pattern: "*.summary" - log: type: file description: Log file recording the core steps of MaxBin algorithm pattern: "*.log.gz" - marker: type: file description: Marker gene presence numbers for each bin pattern: "*.marker.gz" - unbinned_fasta: type: file description: All sequences that pass the minimum length threshold but are not classified successfully. pattern: "*.noclass.gz" - tooshort_fasta: type: file description: All sequences that do not meet the minimum length threshold. pattern: "*.tooshort.gz" - marker_genes: type: file description: All sequences that do not meet the minimum length threshold. pattern: "*.marker_of_each_gene.tar.gz" authors: - "@jfy133"