ANVI'O

Alternatively, if you lack mapping data, you can add the flag so that you can still get the functionality of a profile database... By default, anvi'o will use every contig in your contigs-db. However, if you wish to focus specifically on a subset of these contigs, just provide a file that contains only the names of the contigs you want to analyze, one per line, using the tag ... The flagship anvi'o program to profile a BAM file. Running this program on a BAM file will quantify coverages per nucleotide position in read recruitment results and will average coverage and detection data per contig. It will also calculate single-nucleotide, single-codon, and single-amino acid variants, as well as structural variants, such as insertion and deletions, to eventually stores all data into a single anvi'o profile database. For very large projects, this program can demand a lot of time, memory, and storage resources. If all you want is to learn coverages of your nutleotides, genes, contigs, or..