Microbial 'omics

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

See program help menu or go back to the main page of anvi’o programs and artifacts.

## Usage

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 (...) \


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.

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.