anvi-get-tlen-dist-from-bam

Authors
Can consume
Can provide
Usage
Example run
Output file
Histogram
Additional Resources

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:

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.