The whole-genome sequence (WGS) data for each isolate was aligned to the most recent version of the C. immitis RS3 strain sequence (AAEC02000000) (6 ) by using the software program BFAST (7 ) with the following exclusion criteria: 1) indel-containing reads; 2) reads aligning to multiple locations; and 3) reads with mapping and alignment scores <20 and <100, respectively.
Transcript sequences were aligned to the reference genome using GMAP 2014 02-28 (Genomic Mapping and Alignment Program) [ 37] with the following parameters: −-intronlength = 350000, −-no-chimeras, −-canonical-mode = 1, −-cross-species.
Integrated approaches to synteny mapping and alignment have been proposed, most of which operate on pairs of genomes [8], [25] [27].
Apart from greater ease-of-use, integrated synteny mapping and alignment methods could in theory provide more accurate inference because the alignment can influence the synteny map and vice-versa.
The data was put through our sequencing pipeline consisting of base calling using the Illumina Pipeline, mapping and alignment with BWA [15], PCR duplication removal with SAMTools [16], and GATK [17] for variants calling.
We did not test two-stage pipelines involving separate synteny mapping and alignment steps, such as MERCATOR+MAVID [49] or Chain-net+TBA [50] but this would be an interesting area for future work.
Data mapping and alignment of the original SOLiD WGS sequence data were performed using Life Technologies' (former Applied Biosystems SOLiD Software and Corona Litee suite.
This is done by searching the cDNAs against the rice pseudomolecules using GMAP (the Genomic Mapping and Alignment Program, [ 26]).
MWD conceived and designed the PKW genome sequencing, carried out the read assembly, mapping and alignment, annotation, and variant calling and wrote the manuscript.
The first step in analysing NGS data is mapping and alignment (alignment for short) of the generated small reads to a reference sequence.
