mapping tool for resequencing

glacerda · 04-01-2011, 08:22 AM

Hi colleagues,
Is there any mapping tool that can deal with Illumina mate pair libraries (3Kbp insert, outwards) with up to 50% of paired end 400bp insert inwards contaminating reads?
I would like to use a tool that tries to map a read pair using both options for insert size and orientation. It is also desirable to include in the SAM the reads that map to the genome, even if its pair could not be mapped, flagging it with the proper bits. It is also desirable to include the information if the alignment is unique, multiple, etc.
Do you know any mapping tool that can do all that in just one run?

Thank you

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Bismark - A New Tool for Mapping and Analysis of Bisulfite-Seq Data	fkrueger	Bioinformatics	648	10-05-2018 02:43 AM
Is a Gene mapping tool available?	ritzriya	Bioinformatics	0	02-15-2011 01:45 AM
General mapping rate of human resequencing data against reference in GAiix/Hiseq	cybog337	Illumina/Solexa	2	01-12-2011 09:43 AM
PubMed: BFAST: An Alignment Tool for Large Scale Genome Resequencing.	Newsbot!	Literature Watch	0	11-13-2009 03:10 AM
BFAST: Blat-like Fast Accurate Search Tool for Large-Scale Genome Resequencing	nilshomer	Bioinformatics	1	11-06-2008 10:36 PM

04-01-2011, 08:22 AM	#1
glacerda Member Location: Brazil Join Date: Aug 2008 Posts: 27	mapping tool for resequencing Hi colleagues, Is there any mapping tool that can deal with Illumina mate pair libraries (3Kbp insert, outwards) with up to 50% of paired end 400bp insert inwards contaminating reads? I would like to use a tool that tries to map a read pair using both options for insert size and orientation. It is also desirable to include in the SAM the reads that map to the genome, even if its pair could not be mapped, flagging it with the proper bits. It is also desirable to include the information if the alignment is unique, multiple, etc. Do you know any mapping tool that can do all that in just one run? Thank you