BOL: Question: What are the best way to merge paired end reads ?

Question: Question: What are the best way to merge paired end reads ?

Archana Malhotra
2332 days ago

Question: What are the best way to merge paired end reads ?

I want to merge PE reads. Can you please suggest me good tools.

Answers

I recently used ABySS new program "abyss-mergepairs", source code https://github.com/bcgsc/abyss/blob/master/Align/mergepairs.cc

You can also try USEARCH https://academic.oup.com/bioinformatics/article/31/21/3476/194979

Hope useful.

Jit 2332 days ago

Here is a list of tools which can do the overlapping procedure. I've used one tool (FLASH) to overlap some MiSeq 2x150 PE reads, and then assembled them using Velvet, and the merged reads produced a "better" assembly than with the paired reads. Enjoy!

PEAR (Paired-End Read Merger) http://sco.h-its.org/exelixis/web/software/pear/doc.html

COPE (Connecting Overlapping Paired End reads) http://sourceforge.net/projects/coperead/

SeqPrep https://github.com/jstjohn/SeqPrep

FLASH (Fast Length Adjustment of Short Reads to Improve Genome Assemblies) http://www.cbcb.umd.edu/software/flash

fastq-join (part of ea-utils) http://code.google.com/p/ea-utils/wiki/FastqJoin

PANDAseq https://github.com/neufeld/pandaseq

mergePairs.py http://code.google.com/p/standardized-velvet-assembly-report/source/browse/trunk/mergePairs.py

Rahul Nayak 2317 days ago