scartrek 0.1.0

Python package for identifying gene disrupting and restoring indels in whole-genome sequencing data of Mycobacterium tuberculosis samples

ScarTrek

Python package for identifying gene disrupting and restoring indels in whole-genome sequencing data of Mycobacterium tuberculosis samples

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"Insertion" or "deletions" (affectionly called "indels") of nucleotides are two types of genetic changes besides single nucleotide polymorphims (SNPs) that can be detected by analyzing sequencing data. ScarTrek is an application written in python to detect indels in whole-genome sequencing data mapped to a reference genome, and if gene information for the referece organism is provided, then determine the genes that have the indels and if the indels influence the translated product of the gene. This analyses is useful to detect gene inactivations due to indels.

Additional scripts are provided to do the following upstream analyses: quality control of raw reads in fastq format and mapping the filtered reads to the reference genome. Although, the user will need to install (or load in their environment) third party bioinformatics tools to process fastq files and map the reads. High Performance Computing Centers at major universities already have these resources installed.

For any questions, comments, or suggestions, please contact Aditi Gupta, ag1349 at njms.rutgers.edu or aditi9783 at gmail.com.