genome assembly polisher that can use Sanger reads?

ssully · 03-20-2019, 11:25 AM

We have a PacBio final assembly that requires some polishing to fix e.g. erroneous stop codons. No Illumina reads at hand but we do have a set of high quality Sanger reads from an older version of the genome. Is there a tool like Racon but can use Sanger reads to correct small errors in an assembly?

JTH-Genome · 06-27-2019, 10:55 AM

You could try to modify one of these error correction algorithms: http://wgs-assembler.sourceforge.net...index.php/PBcR

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Genome Res De novo bacterial genome sequencing: millions of very short reads assembly	b_seite	Literature Watch	1	10-05-2017 12:26 AM
Dataset with Ion reads and Illumina/Sanger reads is needed	paraslonic	Ion Torrent	0	10-30-2015 07:55 AM
Denovo assembly combine Ilumina PE reads and sanger reads	bobo xin	De novo discovery	4	11-01-2013 07:35 AM
The best genome de novo assembly software using hybrid data (Illumina, 454 & Sanger)?	Godevil	De novo discovery	36	08-01-2012 03:25 AM
Best tool to map 454 reads onto sanger reads?	dan	Bioinformatics	3	07-27-2009 09:51 AM

03-20-2019, 11:25 AM	#1
ssully Member Location: NYC Join Date: Aug 2010 Posts: 48	genome assembly polisher that can use Sanger reads? We have a PacBio final assembly that requires some polishing to fix e.g. erroneous stop codons. No Illumina reads at hand but we do have a set of high quality Sanger reads from an older version of the genome. Is there a tool like Racon but can use Sanger reads to correct small errors in an assembly?

06-27-2019, 10:55 AM	#2
JTH-Genome Junior Member Location: USA, NC Join Date: Apr 2019 Posts: 6	You could try to modify one of these error correction algorithms: http://wgs-assembler.sourceforge.net...index.php/PBcR