For ABI SOLiD data, two types of mismatches --- the sequencing errors on color space and the mismatches caused by nucleotide polymorphism, should be differentiated.
We designed several groups of multiple spaced seeds to guarantee 100% sensitivity in efficient way. ZOOM doesn’t translate color space reads into base space since there will be error propagation. ZOOM developed a new algorithm to align color space reads directly to the reference nucleotide genome. The sequencing errors in color space reads are corrected automatically along with the mapping process. All possible alignments of each read are checked, so the users can choose to output the uniquely mapped reads or the best N mapping reads of each read. Paired-end reads have been supported. The part supporting insertion/deletion and quality scores are still unstable. So we’ll include these two parts in our next release. Color space reads can be decoded into base space after mapping, with the nucleotide polymorphisms and the sequencing errors highlighted respectively. The assembly related functions are the same with that for Illumina data.
Originally posted by ECO
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