In addition to the tests above, we were interested in evaluating to what extent AlignGraph can improve the genome sequence generated with another reference assisted assembly approach.
For reference assisted assembly sequence reads were aligned on reference genome (H37Rv) using bowtie2 program [ 25] with standard parameters (bowtie2 -x H37Rv - p30 -U raw_reads.fq -S aligned_reads.sam).sam
Alternatively, the genome sequence from a related model organism can be used in the assembly of short read data from the focal species, a process known as reference guided (or reference assisted) assembly [ 31, 32].
We report the result of SOAPdenovo, which is a representative for de Bruijn graph based short read assemblers and its result is comparable to several of other assemblers of the same kind, such as MetaVelvet [ 39], used for metagenomic data sets, and Velvet Columbus [ 22], used for reference assisted assembly.
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An Indigenous reference group assisted with all aspects of the study.
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Such an approach of contextually ordering the reference sequence assisted by GBS maps will, in turn, enable better SNP calling in future GBS datasets and haplotypic imputation of missing data (Poland et al. 2012; Tortereau et al. 2012).
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