Figure 1.
The work-flow of the ISMU pipeline.
The work-flow of the ISMU pipeline is mainly divided into three steps: (A) Data import, quality pre-processing, (B) Sequence alignment and SNP discovery, and (C) Visualization and generation of input files for genotyping assay.
Table 1.
Details about whole genome re-sequencing (WGRS) dataset used for evaluation of the pipeline.
Table 2.
Restriction site associated DNA (RAD) sequence dataset used for evaluation of the pipeline.
Table 3.
RNAseq dataset used for evaluation of the pipeline.
Figure 2.
A snapshot on SNPs in four chickpea genotypes compared to the reference genome.
The Venn diagram shows distribution of SNPs detected between four genotypes (Pistol, Hat Trick, Slasher and Genesis 90). The genotype CDC Frontier was used as a reference sequence. For instance, a total of 95,329 SNPs were found to be concordant between Pistol and Hat Trick genotypes. Similarly, amongst all the four genotypes 62,291 SNPs were found to be in common.
Table 4.
Pairwise SNP distribution between genotypes identified in RAD dataset.
Table 5.
Run time profile of the ISMU pipeline with three datasets (WGRS, RAD and RNAseq).
Table 6.
Comparison of key features of the ISMU pipeline with similar pipelines.