SSRgenotyper : A New Bioinformatics Tool for Genome Re-sequencing Data

-Koustav Maiti, Ramakrishna Mission Vivekananda Centenary College, Rahara

SSRgenotyper is the SSR (Simple Sequence Repeat) genotyping platform that provides scientists with re-sequence data i.e. whole genome or reduced representational data. SSRs are the microsatellites or simple tandem repeats that are used as genetic markers for genetic markers in the biological field. They are short, multiple-time repeated DNA sequences and very prone to mutation.

SSR genotyper (in python 3) needs 3 positional arguments. These are SSR reference FASTA files, a text file for enlisting names of SAM files, and lastly the output name for the results. It can recognize the boundaries of SSR repeat, verify the SSR with an ideal match to the reference, compute the total length of repeated nucleotide and regulate the allele call. The followings are the optional arguments for refining the genotype calling algorithms :

1. Support. : This is the minimum number of supporting reads for a genotype called SSR locus. The genotype data will be seen as missing if the total number of reads is less than the threshold.

2. Minor Allele Het. : This is the least percentage threshold of reads for a small allele of a genotype reviewed as heterozygous.

3. Border Seq. : This is the number of nucleotides of each side of the reference SSR motif.

4.Spurious Allele Removal. : Ambiguous genotypes can result from spurious alleles. These alleles should be least in frequency and should be removed for perfect genotyping.

5. Mismatch. : This is the total number ofmismatches permitted in the border sequence region of the reads and the reference sequences.

SSRgenotyper also gives different data filtering options. This option gives files based on the percentage of missing data :

1. Filter Data Loci. : This is the maximum missing data threshold to describe the SSR locus.

2. filter Data Sam. : This is the maximum missing data threshold to outline an individual SAM file.

Different types of output files are produced by SSR genotyper. They are :

1. The SSR file. : This is the basic genotypic results file in a table with SSR loci in rows and SAM files in columns. The genotypes are termed as alleles that make the repeat units found in each of SSR locus.

2. The .ssrstat file. : This file offers a basic run including genotypic statistics and a listing of positional and optional arguments.

3. The .pop file. : GENEPOP-formatted file is produced by extracting the Genepop arguments. GENEPOP is a very popular program used for testing Hardy-Weinberg tests, population proliferation, linkage disequilibrium, and gene flow estimates. 

4. The .map file. : This file is a tab-delimited table with SSR loci in rows and SAM files in columns.

5. The Alignment file. : This type of file is very useful for spot-checking alignments along with specific genotypic calls.

SSRgenotyper gives us a very good and easy-to-use platform for re-sequencing any data and it is free to use. The accuracy rate of this tool is very high. This kind of tool is a boon to each scientist and researcher in almost every field of biology.

Source: SSRgenotyper: A simple sequence repeat genotyping application for whole‐genome resequencing and reduced representational sequencing projects; Daniel H. Lewis, David E. Jarvis and Peter J. Maughan; Applications in Plant Sciences; 3^rd December 2020; Volume 8; Issue 12; doi: DOI: 10.1002/aps3.11402