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Sep 7, 2021
Sep 7, 2021

Welcome to Computel v1.3!

Computel is designed for measuring mean telomere length and abundance of canonical and variant telomeric repeats from Illumina Whole Genome NGS Sequencing data.

Operating Systems

Computel versions > v0.3 work with Unix operating system (tested for Ubuntu Linux). Computel version v0.2 works with Windows and Unix operating systems, however this version is harder to apply.

Installation

For installation download and uncompress the Computel package in a local directory. The required binaries and files for setup configuration are set in the package. Make computel.sh executable by running 'chmod +x computel.sh'.

Test run

To test how this works navigate to computel directory and run:

./computel.sh -1 src/examples/tel_reads1.fq.gz -2 src/examples/tel_reads2.fq.gz -o mytest

A successful test run, should return telomere length of 10683991 bp. You should get a warning that the coverage is low: this is ok for the test run, as the example files are of low coverage.

Usage

The basic usage is:

./computel.sh [options] -1 <fq1> -2 <fq2> -o <outputpath>

Please, check the manual for advanced options.

Output

Computel's main output are two files in output directory:

  • tel.length.txt - a tab delimited text file containing mean telomere length (bp) values and other parameters
  • tel.variant.txt - a tab delimited text file containing absolute and relative amounts of telomeric repeat variants.

System requirements

You have to have R (version 3.0.3 or higher) and samtools version 1.3 or higher (for Computel v0.4) installed in your system.

Binaries

Note, Computel works with only some versions of Bowtie, and with Samtools version 1.3 or higher. You can specify your own binaries with respective options, however, you may first want to refer to the Computel User Manual.

Releases

Version 1.3 let's the user set the reference genome index to align non-telomeric reads and for more accurate base coverage estimation

Version v1.2 allows to change the quality threshold (default being Phred+33 25)

Version v1.1 computes telomeric variants with Phred+33 25 qual threshold.

Version v1.0 has an additional feature of computing the relative abundance of telomeric canonical and variant repeat patterns among the telomeric reads.

Version v0.4.1 has fixed a minor bug from the v0.4 release.

Version v0.4 works with shell script and has a straightforward usage. This version of Computel uses the samtools (version 1.3 or higher) installed on the user's system, instead of the precompiled version coming with the previous releases.

Version v0.3 works with shell script and has a straightforward usage.

Version v0.2 works also with compressed fastq files.

Version v0.1 works both Windows and Unix type operating systems, works with configuration files and Rscript. Works also with compressed fastq files.

Citation

Use the following citation to read about our software, and cite it in your research:

Nersisyan L, Arakelyan A (2015) Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data. PLoS ONE 10(4): e0125201. doi:10.1371/journal.pone.0125201

Feedback

This is the betta version of the software: your feedback at this point is critical for its further development! Please, join the Computel discussion group at https://groups.google.com/forum/#!forum/computel-discussion-forum, and add your comments. Please, do not hesitate to share any inconvenience you face with our software, any bug you notice and any suggestion you have.

If you're happy with Computel, let us know - make us happy too!

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Compute mean telomere length from Whole Genome Sequencing data.

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