Day Two

DAY TWO 9:00 – 9:10Recap of day one 9:10 – 9:55TOPAAS demo (Sander) 9:55 – 10:15Coffee break 10:30 – 11:30New Technology Data 11:30 – 12:30High Repeat Content Clones 12:30 – 13:30Lunch 13:30 – 14:30Alternative chemistry SIL and TIL library utilisation 14:30 – 15:00Available Tools and Databases on SGN (Lukas) END

Issues Arising  Criteria for `unmapped` BAC procedure added to standards document – include IL mapping centrally  Trace file submission and naming convention – needs further discussion  SBM Blast server available for data mining the Selected BAC Mixture Shotgun - add consensus values to the contigs to increase utility  Some BACs remain at Phase 2 due to complex repeats  Cases of potential deletion/ duplication in Korea Chrm 2 set  Overlap criteria and checks added to the standards document

Use of restriction digest data  Not all groups currently make use of restriction digest data  Lukas to investigate central Restriction Digest Resource  Mail to PIs for agreement for making a requirement or not Use of misc_feature tags  Not all groups currently use this system  Reduce list down to essential misc_feature tags  Mail to PIs for agreement

TOPAAS – Sander Peters

New Technology Data Types 454 runs have been done not submitted Both Illumina and SOLiD planned How do we submit this data to HTGS? Do we need to make the data type distinction clear? Small read storage will be an issue.

International Finishing Standards Discussion Attempting to capture information about the sequence type etc There are no agreed quality scores for the New Tech Data

Categories and Current Assigned Codes 1. Technology – order is ~chronological in terms of WTSI usage A – Slab Gels (AB 373, AB 377) B - Megabase C – Capillary (AB 3100, AB 3700, AB 3730) D – 454 E – Solexa F – ABI Solid 2. Data Coverage This will be represented as a numeric value in accordance with how much coverage there is over the target sequence. 3. Assembler – order assigned is arbitrary A – Newbler (454) B – Arachne C – Phrap D – Phusion-phrap E – Cemos F – Mosaic (combined assembly) G – Sakke (solexa) etc 4. Post-shotgun Intervention – currently divided into broad tasks – the finer definition will see more division between Eukaryotes and Prokaryotes. A – No post-shotgun intervention at all B – Targeted finishing (contig or specific loci) C – Contiguate D – Not contiguous but contigs ordered and orientated E – Automated Sequence Improvement F – Manual Intervention with no chemistry G – Finished for prokaryotes – Sequence Improved for eukaryotes H – Finished clone or chromosome

Life after the workshop……. Brief Workshop report and minutes to be written up Lukas to re-circulate standards documents to group Add section to the next newsletter Await decision on digests and misc_feature tags Have a safe journey home and thank you all for your effort and input

Consortium have been set up since 2005 Promoting a schema for minimum information about a genome sequence and metagenome samples/sequences MIGs and MIMs May prove useful for comparative sequencing – very applicable to pathogen genomes