Reports sequences stored in one or more BAM files that cover one of more specific nucleotide positions in a reference.

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Reports sequences stored in a bam-file file that cover one of more specific nucleotide positions in a reference.

Basic mode of operation

Assume you wish to recover reads stored in one or more BAM files, where the matching reads contain at least one nucleotide position that align to a nucleotide position nucleotide_position_N in a contig contig_name_X. In that case, the user would first generate a two column TAB-delmited file, for example positions_for_linkmers.txt with no header line,

contig_name_X nucleotide_position_N

And run the program this way to recover the short reads from this way:

anvi-report-linkmers --contigs-and-positions positions_for_linkmers.txt \
                     -i SAMPLE_01.bam SAMPLE_02.bam SAMPLE_03.bam (...) \
                     -o linkmers.txt

The user can define multiple contigs in the input file, and one or more nucleotide positions for each one of them:

contig_name_X nucleotide_position_01,nucleotide_position_02,nucleotide_position_03
contig_name_Y nucleotide_position_04
contig_name_Z nucleotide_position_05,nucleotide_position_06

The resulting linkmers-txt would include all short reads that match any of these critera

Using the --only-complete-links flag, the user can enforce whether only complete links should be reported where each reported short read must cover each nucleotide position for a given contig.

Please note that if the nucleotide positions chosen for a given contig are too distant from each other given the short read length, zero reads may satisfy the complete links criterion.

Having complete links, however, will enable oligotyping analyses on metagenomic reads through the anvi’o program anvi-oligotype-linkmers.

See this program in action

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Additional Resources

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