Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
software for genome assisted scaffolding sasignor Bioinformatics 4 08-14-2012 05:08 PM
Assisted de novo genome assembly? Create new consensus mapping reads to reference? zmartine Bioinformatics 8 02-10-2012 01:31 AM
PubMed: Sequence-based physical mapping of complex genomes by whole genome profiling. Newsbot! Literature Watch 0 07-14-2011 03:00 AM
Assisted assembly of contigs into supercontigs/chromosomes lechu502 Genomic Resequencing 1 12-13-2010 05:56 AM
PubMed: ALLPATHS: De novo assembly of whole-genome shotgun microreads. Newsbot! Literature Watch 0 03-15-2008 06:46 AM

Thread Tools
Old 05-20-2013, 11:03 PM   #1
Location: china

Join Date: Sep 2012
Posts: 10
Default Physical map-assisted whole genome shotgun assembly

Hi all,

My question is how to intergrate BAC-end senquencing reads with contigs from WGS. Is there any tools can do this job ?
I have a phyical map with BAC-end sequencing reads , BAC contig orders from BAC fingerprint, and some contigs of assembly result from WGS.
juckdnarocks is offline   Reply With Quote
Old 05-21-2013, 03:46 PM   #2
Senior Member
Location: Adelaide, Australia

Join Date: Sep 2010
Posts: 119

Are the BAC contigs from Fingerprints (ie. Physical Contigs) ordered?

My guess would be that if you have a physical map that has been constructed and ordered along chromosome scaffolds, then you would have all BAC locations along your physical map. This means that you can just match the BAC address of the BAC-end sequence (the read names should match) and then anchor WGS contigs to that.

Unfortunately there are no real tools to do this, but it is easily done using a small script and BLAST. You need to match BAC-ends to BACs within the physical contigs, and then use BLAST to match BAC-end sequences to a WGS contig
jimmybee is offline   Reply With Quote

bac-end sequencing, phyisical map, wgs

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:50 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO