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Sequencing

• How big is the Stagonospora nodorum genome?
• What strain was sequenced?
• What is the current state of the assembly?
• How has the sequence been generated for the Stagonospora nodorum project?
• Will the genome be finished?
• How will we know the assembly is correct?
• What data are available?
• This sequence release looks different from previous releases, like Neurospora crassa. What's different?
• What are the plans for annotation?

Misc

• How do I cite the sequence for publication?
• Who do I contact with questions about the sequencing?

Sequencing

1. How big is the Stagonospora nodorum genome?
   

   Our current total unique contig length is 37,071,112 bp (base pairs). The estimated genome size of S. nodorum is 37.1 Mb.

2. What strain was sequenced?
   

   Stagonospora nodorum strain SN15.

3. What is the current state of the assembly?
   

   The current assembly contains 496 sequence contigs in 109 supercontigs (scaffolds). There are no current plans for additional sequencing or finishing. See Assembly for detail.

4. How has the sequence been generated for the Stagonospora nodorum project?
   

   Our data consist of over 370,000 individual sequencing reads obtained by sequencing each end of plasmids and Fosmids from libraries containing randomly sheared fragments of 4 kb, 10 kb, and 40 kb average size respectively. See Assembly for details.

5. Will the genome be finished?
   

   Unfortunately there are no plans to finish this genome at this time.

6. How will we know the assembly is correct?
   

   The quality of the assembly will be assessed in several ways. In addition to requiring that the paired plasmid and Fosmid ends occur in a logical manner, our assembly of the Stagonospora nodorum genome will be verified through comparison with available genomic sequences.

7. What data are available?
   

   In this version of our data release, all sequence contigs and supercontigs are available. Sequence data can be accessed in several ways: either through a searching with BLASTN or TBLASTN, retrieving of a specific region of the assembly, or by downloading the entire genome. Supercontig and contig sequences are subject to change throughout this project, so each data release version number will be appended to the contig number as a prefix (e.g. 1.1 denotes assembly version 1, supercontig #1).

   Fosmid clones have been integrated into the current assembly, and you can search and view the locations of these clones within the sequence supercontigs.

   A fasta file of raw reads excluded from the assembly is also available for BLAST and download. Also available for download are an AGP file describing the supercontigs and contigs in this assembly and a file listing coordinates of paired endreads.

8. This sequence release looks different from previous releases, like Neurosprora crassa. What's different?
   

   Important information about this release can be found here.

9. What are the plans for annotation?
   

   An automated annotation is now available.

Misc

1. How do I cite the sequence for publication?
   

   Publications should include the following citation:
   Stagonospora nodorum Sequencing Project. Broad Institute of Harvard and MIT (http://www.broad.mit.edu)

2. Who do I contact with questions about the sequencing?
   

   Our email address is annotation-webmaster(at)broad.mit.edu.