co-assembly bam file generation for metagenomic binning

[Former user]

Will it make a difference to generate the BAM files individually for each sample in a co-assembly vs using a cat of all the samples into one.

I can't think of any reason why it would make a difference but I am not very familiar with this.

[Rob Egan]

One of the more powerful metrics that metabat uses is differential abundance of the sequences across samples, so it is very important to have separate BAM files for separate samples (i.e. physical samples with time, space or other differences that may lead to differing abundances, as opposed to simple aliquots from the same sample).

The benefits of this differential abuncance is highlighted in our papers.