Introduction

Homopolymer (HP) sequencing is error-prone in next-generation sequencing (NGS) assays, and may induce false insertion/deletions and substitutions. DNA homopolymer (HP) tracts, also known as mononucleotide microsatellites, are sequences consisting of a series of consecutive identical bases, such as poly(dA).poly(dT) and poly(dG).poly(dC), which are the simplest of the sequence repeats in the genome. This program aimed to identify the specific homopolymeric sequences.

Manual

Dependencies:

• python3
• numpy

Install Using Bioconda:

conda create -n python3 -c conda-forge -y
conda install python=3
conda install conda-forge::numpy

Useage

To run ArtifactsFinder

python3 homoploymer_finder.py Sample.recal.bam Sample input.site.xls test

Note : Sample.recal.bam is the input bam file; Sample is the sample name; input.site.xls is the input specific homopolymeric sequences file; test is the prefix in the output results name (Sample.prefix.homoploymer.repeat.xls,Sample.prefix.homoploymer.all.xls)

Input File

bam file

An example of a bam file can be viewed here: ([`Sample.recal.bam`](HomoploymerFinder/example/Sample.recal.bam)).

Note: Must have an index file for bam.

specific homopolymeric sequences file

An example of a specific homopolymeric sequences file can be viewed here: ([`input.site.xls`](HomoploymerFinder/example/input.site.xls)).

Output File

sam file

An example of a sam file can be viewed here: ([`Sample.sam`](HomoploymerFinder/example/Sample.sam)).

Note: The sam file is extract bam from specified region. Here is the bam of the last region in the input homopolymeric sequences file.

Sample.test.homoploymer.repeat.xls

An example of a Sample.test.homoploymer.repeat.xls file can be viewed here: ([`Sample.test.homoploymer.repeat.xls`](HomoploymerFinder/example/Sample.test.homoploymer.repeat.xls)).

Note: The results which satisfy left sequence, right sequence, and insert sequence contains one or more repeating unit of target repeated sequences.

Sample.test.homoploymer.all.xls

An example of a Sample.test.homoploymer.all.xls file can be viewed here: ([`Sample.test.homoploymer.all.xls`](HomoploymerFinder/example/Sample.test.homoploymer.all.xls)).

Note: The all results which satisfy left sequence, right sequence. The insert sequence may contains repeating unit of target repeated sequences and other bases.

###Contact If you have any questions, please contact lilicai@chosenmedtech.com .