SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Aligning Illumina paired-end data with read length 250 bp opulcy97 General 31 04-10-2015 03:55 PM
EBARDenovo - A new RNA-seq do novo assembler for paired-end Illumina data htchu.taiwan RNA Sequencing 2 06-10-2013 12:13 AM
EBARDenovo - A new RNA-seq do novo assembler for paired-end Illumina data htchu.taiwan Illumina/Solexa 9 04-15-2013 11:08 PM
searching 454 (single read) + Illumina paired-end or matepair data boetsie General 0 10-04-2010 01:45 AM
Paired end Short read data SS1234 Bioinformatics 6 06-09-2010 01:16 PM

Reply
 
Thread Tools
Old 05-06-2018, 02:01 PM   #1
michaelbarton
Junior Member
 
Location: Oakland, CA

Join Date: Jan 2010
Posts: 9
Default Sharing benchmarking results for short read assembler on paired end Illumina data

We recently wrapped up some work on benchmarking the more recent genome assemblers on a range of genomes with Illumina paired end sequence data. We compared a few of the most common metrics, one metric we included was the number of correct genes in an assembly. The overall best assembler for this metric was the JGI isolate assembly pipeline which used BBMap preprocessing steps and spades as the assembler.

The outline of this is here:

http://www.bioinformaticszen.com/pos...mbly-software/

A github repo for a docker image with this assembler is here:

https://github.com/bioboxes/jgi-isolate-pipeline
michaelbarton is offline   Reply With Quote
Old 09-11-2018, 12:24 PM   #2
pepperoni
Member
 
Location: US

Join Date: Oct 2011
Posts: 58
Default

Would you recommend the pipeline for large genomes (100Mb) ?
pepperoni is offline   Reply With Quote
Reply

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 04:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO