Microbial 'omics


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anvi-get-tlen-dist-from-bam [program]

Table of Contents

Report the distribution of template lengths from a BAM file. The purpose of this is to get an idea about the insert size distribution in a BAM file rapidly by summarizing distances between each paired-end read in a given read recruitment experiment..

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Can consume

bam-file

Can provide

This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.

Usage

This program may be useful if you are interested in learning the insert size distribution in a given bam-file.

Example run

The most straightforward way to run the program is the following:

anvi-get-tlen-dist-from-bam bam-file

Here is an example output in the terminal:

BAM file .....................................: ./INVERSION-TEST/CP_R03_CDI_C_07_POST.bam
Number of contigs ............................: 8
Number of reads ..............................: 2,331,062
Minimum template length frequency ............: 10
Maximum template length to consider ..........: 500,000


WARNING
===============================================
Some of your contigs, 2 of 8 to be precise, did not seem to have any template
lenght data. There are many reasons this could happen, including a very high
`--min-tlen-frequency` parameter for BAM files with small number of reads. But
since there are some contigs that seem to have proper paired-end reads with
template lengths, anvi'o will continue reporting and put zeros for contigs that
have no data in output files.

Output file ..................................: TEMPLATE-LENGTH-STATS.txt


✓ anvi-get-tlen-dist-from-bam took 0:00:05.483682

Output file

The program will report a TAB-delimited output file with the following format:

contig length num_reads_considered mean mean_Q2Q3 median min max std
B_fragilis_ARW016_000000000001 5526948 2213634 367.6 392.5 393.0 32 71613 663.1
B_fragilis_ARW016_000000000002 3905 634 398.6 398.7 399.0 382 415 7.926
B_fragilis_ARW016_000000000003 4039 588 397.5 397.8 398.0 380 411 7.206
B_fragilis_ARW016_000000000004 3950 524 397.4 397.2 397.0 382 414 7.492
B_fragilis_ARW016_000000000005 911 0            
B_fragilis_ARW016_000000000006 647 0            
B_fragilis_ARW016_000000000007 12247 1860 394.9 396.7 397.0 99 419 23.61
B_fragilis_ARW016_000000000008 4861 528 396.7 396.7 397.0 384 410 6.746

Histogram

If you run the program with the flag --plot, it will attempt to plot a histogram for all contigs in the BAM file.

The plotting function requires an additional Python library, plotext, to be installed. While it is not a part of the default anvi’o distirbution, you can install it in your environment by running pip install plotext.

Here is an example run:

anvi-get-tlen-dist-from-bam CP_R03_CDI_C_07_POST.bam \
                            --plot \
                            --max-template-length-to-consider 5000 \
                            --min-template-length-frequency 2500

And the result in the terminal:

Example output

The histogram may require additional filters to avoid skewed displays due to outliers. The parameters --max-template-length-to-consider and/or --min-template-length-frequency may be useful for such adjustments. Please see the help menu for their details.

The best practice is likely to run the program without any of these parameters and without the --plot flag to generate a comprehensive TAB-delimited report, and then use the --plot flag to visualize trends.

Edit this file to update this information.

Additional Resources

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.