ZOOM released (supporting both Illumina data and ABI SOLiD data)

[spirit]

Hi, ECO. Nice to meet you!

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.

Hey Spirit, Looks nice!

Can you outline your treatment of SOLiD data and colorspace?

[ECO]

Hey Spirit, Looks nice!

Can you outline your treatment of SOLiD data and colorspace?

[spirit]

Hi,

ZOOM is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis.

1. The spaced seed strategy specially extended for short reads mapping problem guarantees 100% sensitivity for a wide range of read length and mismatch numbers.
2. Supports Illumina/Solexa and ABI SOLiD instruments
3. Easily maps reads 15 to 64 bps long
4. Handles both mismatches and insertions/deletions
5. Supports paired-end reads mapping
6. Accounts for read sequence quality scores
7. Reports uniquely mapping results or best N mapping results for each read
8. Integrated multiple sequence alignment for consensus reconstruction and SNP identification.
9. Coverage and heterozygous information for each position of consensus sequence reported.
10. Automatically detect and correct sequencing errors for ABI SOLiD data
11. Decode reads in color space into base space, with sequencing errors and polymorphisms highlighted.

More detailed information and demo version can be found in http://www.bioinfor.com/products/zoom/index.php. Welcome to try it out.

We'll build an on-line server for academic users soon. So please try demo-version first.

For those who are interested, there is some discussion about ZOOM in http://seqanswers.com/forums/showthread.php?t=43&p=1240