Release notes

Version 1.50 (2010-05-14)

The contigs from assembly 1.03 were polished using the SOLiD data and SOLEXA data. Polishing included sinlge-base error correction and indel correction (mostly homopolymer).
Contamination from E.coli and vector sequences was removed. Organellar sequences were separated (and are thus not included in this data set).
Several structural inconsistencies were solved.
Contigs from fully sequences BACs were integrated.
Superscaffolds were built using clone-end information (BAC and fosmid ends).

Contigs (only the contigs that make up the scaffolds): 29,736 sequences, 733.0 Mb, 50% of assembly in 2,754 contigs of 69,257 bp or longer
Scaffolds: 3,584 sequences, 781.2 Mb, 50% of assembly in 27 scaffolds of 7.8 Mb or longer

During the assembly we screened for E. coli sequences to prevent the E. coli contamination (from the SBM data) as found in version 1.0
Two new 454 runs (3kb and 20kb) were added to the assembly
This assembly was made with an updated version of the assembler

A new filtered 454 data set was created because of the addition of 2 new 454 runs (3kb and 20kb)
- 56 million reads, 20.8 Gb, approx. 22.0X coverage
SBM and clone-end input were the same as in version 1.00 (see below)

Contigs: 110,872 sequences, 762.0 Mb, 50% of assembly in 3,641 contigs of 55,730 bp or longer
Scaffolds: 3,761 sequences, 781.7 Mb, 50% of assembly in 52 scaffolds of 4.4 Mb or longer

This assembly contains 454 sequences, Selected BAC clone Mixture (SBM) sequences, and BAC/fosmid end sequences.
- 454 (filtered): 55 million reads, 20.5 Gb, approx. 21.6X coverage
- SBM (filtered): 3.8 million reads, 3.1 Gb, approx. 3.3X coverage
- BAC ends (filtered): 308,490 sequences (incl. 135,271 pairs), 180 Mb, approx. 0.18X coverage
- Fosmid ends (filtered): 151,299 sequences (incl. 64,722 pairs), 83 Mb, approx. 0.087X coverage

Contigs: 118,692 sequences, 762.5 Mb, 50% of assembly in 4,238 contigs of 47,298 bp or longer
Scaffolds: 7,409 sequences, 794.6 Mb, 50% of assembly in 50 scaffolds of 4.5 Mb or longer

454
- approx. 80 runs, 78.6 million reads, 27.7 Gb, approx. 29.2X coverage
- Data sequenced with the GS FLX Titanium
- Approx. 39 runs from WGS libraries, 19 runs from 3 Kb libraries, 12 runs from 8 Kb libraries, and 10 runs from 20Kb libraries, resulting in approx. 20 Gb from WGS reads and 8.3 Gb from paired-end reads
SBM (=Selected BAC clone Mixture)
- 4,039,383 sequences, 4.9 Gb, approx. 5.2X coverage
- Shotgun sequencing from BAC clone pools, using the BAC end sequences available at the SGN website
- http://www.kazusa.or.jp/tomato/
BAC ends: 309,305 sequences, 180 Mb, approx. 0.19X coverage
- BAC ends come from 3 enzyme libraries (HindIII, MboI, EcoRI)
Fosmid ends: 151,301 sequences, 83 Mb, approx. 0.08X coverage
SOLiD: 2 runs 1kb, 2 runs 5kb, 2 runs 10kb, 2 runs 7kb (forward only)
- The SOLiD data has not been used in the assembly yet (up to version 1.03)