Helmholtz Zentrum München - German Research Center for Environmental Health

Release notes

Version 2.40 (2011-02-02)

Changes

In order to meet all of Genbank's requirements and to remove some remaining contamination, the following changes were made:

  • Gaps created during the clone-end scaffolding phase (60 Ns, but actually without a size estimate) have been changed to size 100 and type ′clone′ in the AGP files, suggesting there is evidence linking a clone to sequence on both sides of the gap.
  • Scaffold-breaking gaps of size 100 have been changed to type 'contig' and the linkage is set to ′no′ in the AGP files, which means the few places where scaffolds were linked by the physical maps can't be found back in the AGP files.
  • 4 contigs that were identified as completely mitochondrial have been removed:
    • SL2.31ct07311 (SL2.31sc03785)
    • SL2.31ct15354 (SL2.31sc04414)
    • SL2.31ct21887 (SL2.31sc05620)
    • SL2.31ct24035 (SL2.31sc05997)
  • 3 additional contigs with other contamination have been removed:
    • SL2.31ct15290 (SL2.31sc04354): Cupriavidus metallidurans CH34
    • SL2.31ct19589 (SL2.31sc04952): Methylobacterium extorquens AM1
    • SL2.31ct20418 (SL2.31sc05165): Stenotrophomonas maltophilia K27

The consequences of these changes are that in terms of content very little has changed with respect to v2.31, but that the coordinates of most scaffolds and contigs along the chromosomes have changed. This was necessary to achieve compliance with GenBank's gap-size rules. A mapping between v2.31 and v2.40 is available upon request, but should be used with caution. An updated ITAG annotation for this assembly is forthcoming.

Assembly stats

  • Contigs (only the contigs that make up the scaffolds): 26,877 sequences, 737.6 Mb, 50% of assembly in 2,008 contigs of 87,006 bp or longer
  • Scaffolds: 3,223 sequences, 781.3 Mb, 50% of assembly in 17 scaffolds of 16.5 Mb or longer
  • Pseudomolecules: 12 chromosomes and "chromosome 0", 781.6 Mb. 91 scaffolds placed on chromosome 1 to 12, 53 of these are also oriented.

Version 2.30 (2010-08-09)

Changes

  • Sequenced BACs were integrated in the scaffolds of assembly version 2.10.
    • Version 548 of tomato BAC sequences (downloaded from SGN) was used as the basis for BAC integration. Phase 1 BACs (23.2 Mb) were excluded. Phase 2 and phase 3 BACs were assembled into contigs and further processed for the integration, resulting in 117.5 Mb of sequence.
    • Out of the available 117.5 Mb of BAC sequence, 116.6 Mb was integrated. During the integration 4.5 Mb of Ns in the assembly were replaced by real DNA sequence.
    • For further information see the "BAC integration summary".
  • After the BAC integration the scaffolds were ordered and oriented on the 12 chromosomes using the two physical maps (Keygene WGP and Arizona SNaPshot), the Kazusa genetic map, and multiple FISH maps.

Technical details

  • The new scaffolds were placed and oriented on the 12 chromosomes by integration of the two physical maps (Keygene WGP and Arizona SNaPshot), the Kazusa genetic map, and multiple FISH maps.
    • Where possible, the scaffolds were placed and oriented on one of the 12 chromosomes. Corresponding MULTI-FASTA and AGP files were produced. Unoriented scaffolds have "0" as orientation in the AGP files and have the "+" orientation in the corresponding FASTA files. Scaffolds linked by the physical maps have "yes" in the linkage column in the AGP files. Gaps between adjacent scaffolds on chromosomes are of type "U" (undefined size) and size 100 (following the NCBI specifications).
    • Intra-scaffold gaps, linking two contigs, that were produced during clone-end scaffolding with Bambus, are of size 60 and type "U". The real size of these gaps are unknown.
    • All scaffolds that could not be placed on either of the 12 tomato chromosomes by either the genetic or physical maps were placed on an artificial "chromosome 0". The scaffolds on this chromosome are ordered from large to small and unoriented.
    • All sequences are in upper case.
    • The orientation of all contigs in the scaffolds is always "+" because the contigs are reconstructed from the scaffolds.
    • The orientation of all contigs in the chromosomes is either "+" or "-", never "0", as the contigs have an order and orientation in the scaffolds.

Assembly stats

  • Contigs (only the contigs that make up the scaffolds): 26,874 sequences, 737.7 Mb, 50% of assembly in 1,996 contigs of 87,129 bp or longer
  • Scaffolds: 3,232 sequences, 781.4 Mb, 50% of assembly in 17 scaffolds of 16.5 Mb or longer
  • Pseudomolecules: 12 chromosomes and "chromosome 0", 781.7 Mb. 91 scaffolds placed on chromosome 1 to 12, 53 of these are also oriented.

Version 2.10 (2010-06-25)

Changes

  • The scaffolds from assembly 1.50 were further linked together by the clone ends (BAC and fosmid)
  • The new scaffolds were placed and oriented on the 12 chromosomes by integration of the two physical maps (KeyGene WGP and Arizona SNaPshot), the Kazusa genetic map, and multiple FISH maps.
    • Where possible, the scaffolds were placed and oriented on one of the 12 chromosomes. Corresponding MULTI-FASTA and AGP files were produced. Unoriented scaffolds have "0" as orientation in the AGP files and have the "+" orientation in the corresponding FASTA files. Scaffolds linked by the physical maps have "yes" in the linkage column in the AGP files. Gaps between adjacent scaffolds on chromosomes are of type "U" size) and size 100 (following the NCBI specifications).
    • All scaffolds that could not be placed on either of the 12 tomato chromosomes by either the genetic or physical maps were placed on an artificial "chromosome 0". The scaffolds on this chromosome are ordered from large to small and unoriented.
    • All sequences are in upper case.
    • The orientation of all contigs in the scaffolds is always "+" because the contigs are reconstructed from the scaffolds.
    • The orientation of all contigs in the chromosomes is either "+" or "-", never "0", as the contigs have an order and orientation in the scaffolds.

Assembly stats

  • Contigs (only the contigs that make up the scaffolds): 29,736 sequences, 733.0 Mb, 50 % of assembly in 2754 contigs of 69,257 bp or longer
  • Scaffolds: 3433 sequences, 781.3 Mb, 50% of assembly in 17 scaffolds of 16.5 Mb or longer
  • Pseudomolecules: 12 chromosomes and "chromosome 0", 781.6 Mb

Version 2.00 (2010-06-16)

Version 2.00 was retracted because of some technical errors in the data. Please do not use version 2.00 for any analysis.

Changes

  • The scaffolds from assembly 1.50 were further linked together by the clone ends (BAC and fosmid)
  • The new scaffolds were placed and oriented on the 12 chromosomes by integration of the two physical maps (KeyGene WGP and Arizona SNaPshot), the Kazusa genetic map, and multiple FISH maps.
    • Where possible, the scaffolds were placed and oriented on one of the 12 chromosomes. Corresponding MULTI-FASTA and AGP files were produced. Unoriented scaffolds have "0" as orientation in the AGP files and have the "+" in the corresponding FASTA files. Scaffolds linked by the physical maps have "yes" in the linkage column in the AGP files. Scaffolds linked by the physical maps have "yes" in the linkage column in the AGP files. Gaps between adjacent scaffolds on chromosomes are of type "U" (undefined size) and size 100 (following the NCBI specifications).
    • All scaffolds that could not be placed on either of the 12 tomato chromosomes by either the genetic or physical maps were placed on an artificial "chromosome 0". The scaffolds on this chromosome are ordered from large to small and unoriented.

Assembly stats

  • Contigs (only the contigs that make up the scaffolds): 29,736 sequences, 733.0 Mb, 50%25 of assembly in 2,754 contigs of 69,257 bp or longer
  • Scaffolds: 3,433 sequences, 781.3 Mb, 50%25 of assembly in 17 scaffolds of 16.5 Mb or longer
  • Pseudomolecules: 12 chromosomes and "chromosome 0", 781.6 Mb

Version 1.5 (2010-05-14)

Changes

  • The contigs from assembly 1.03 were polished using the SOLiD data and SOLEXA data. Polishing included single-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).

Assembly stats

  • 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

Version 1.03 (2010-01-22)

Changes

  • 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

Assembler

  • This assembly was made with Newbler version 2.3-PostRelease-01/11/2010

Assembly input

  • 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)

Assembly stats

  • 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

Version 1.00 (2009-11-27)

Assembler

  • This assembly was made with Newbler version 2.3-PostRelease-11/19/2009

Assembly input

  • 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

Assembly input

  • 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

Raw data

  • 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 3kb libraries, 12 runs from 8kb 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)
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