are a BAM files mandatory ?

[Former user]

In the paper, the mapping of the sequences are mentioned as pre-requisite, sound like mandatory. The command line examples (runMetaBat.sh <options> assembly.fasta sample1.bam [sample2.bam ...] or metabat2 -i assembly.fasta -a depth.txt -o bins_dir/bin) and benchmarks in the documentation include the depth file or used the bam files. But the -a flag it is not an obligatory requirement (optinal) to run metablat, for example: metabat2 -i assembly.fasta -o bin apparently run well and generates binning as well. My questions are: 1- How influences metablat results if we run it without the bam or depth file ? 2- What is the use of the bam files in the algoritm ?

[Rob Egan]

Please read the README and the paper if you are interested in the algorithm. The abundance correlation is given by the coverage depth that the BAM files reveal. The Tetra-nucleotide frequencies are derived from the sequences in the fasta file, and MetaBAT works best with both are available.