High-throughput genotyping software for short reads

(1) Convert Solexa sequences to Sanger fastq files, 
naming them with the style like "lane1.AAT.fastq".  
Here, "Lane1" is the lane used for sequecing the RIL, 
and "AAT" is the tag for a particular RIL.

To convert Solexa sequences to Sanger fastq, 
you can go to MAQ page and download the maq:
http://maq.sourceforge.net/

maq sol2sanger YourRaw.fastq lane1.AAT.fastq


(2) The genotype assignment pipeline to deal with ssaha2 alignment result.

The fastq seuqences should be aligned with both genomes first using Ssaha2,

./ssaha2 -rtype solexa -kmer 13 -skip 2 -score 30 -diff 0 -depth 500 -align 0 -pair 50,900 ./Parent1_genome.fa $Lane.$Tag.PE.fastq > $Lane.$Tag.PE.fastq.p1

./ssaha2 -rtype solexa -kmer 13 -skip 2 -score 30 -diff 0 -depth 500 -align 0 -pair 50,900 ./Parent2_genome.fa $Lane.$Tag.PE.fastq > $Lane.$Tag.PE.fastq.p2

and then run the genotype assignment pipeline:

perl Step1.pl Lane1 AAT 36

Here "36" is the length for your reads.

Make sure the Ssaha2 has been installed in your computer. 
To get the Ssaha2 package, please go to Ssaha2 page and download them:
http://www.sanger.ac.uk/Software/analysis/SSAHA2/


(3) The genotype calling pipeline to get recombination map.

perl Step2.pl Lane1.AAT.PE.fastq.rlt Genome_length_list PCR_marker_list RIL_001

Here, genome_length_list is the genome length list of the organisms. 
PCR_marker_list is your PCR marker result [optional]. 
Lane1.AAT.PE.fastq.rlt and RIL_001 are input and output files, respectively.



Thank you for your interest in our high-throughput genotyping software.
