SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Input files for the Celera Assembler? dan Bioinformatics 19 02-05-2014 06:38 AM
assemble fasta by Celera Assembler shuang Bioinformatics 1 02-14-2012 05:58 AM
Celera Assembler seems to discard HiSeq reads benikaj Bioinformatics 0 11-08-2011 01:33 PM
Problem with Celera Assembler sram Bioinformatics 6 09-14-2011 04:00 AM
Celera Assembler runCA failed DNAjunk Bioinformatics 2 09-08-2009 04:52 AM

Reply
 
Thread Tools
Old 03-16-2012, 11:49 AM   #1
wichne
Junior Member
 
Location: Los Angeles, CA

Join Date: Feb 2012
Posts: 2
Default Celera assembler and metagenomic data - no contigs?

Hi, I'm trying to assemble some 100bp paired-end illumina reads using CA-7.0.

The run did not fail, but resulted in no contigs. 70% of my reads were, however, in degenerate contigs.

Is this expected because of a) short read lengths b) replicate sequences c) variation in the natural population d) all of the above (plus other stuff not listed)?

I did an assembly of a subset of this data that went together quite nicely.

thanks,
Bill

specfile:
Code:
fakeUIDs      = 1  #default 0

#  TRIMMING
vectorTrimmer  =  ca  # default ca; others figaro, umd
doOverlapBasedTrimming = 1 # default 1
obtOverlapper   =  ovl
mbtConcurrency = 4
mbtThreads = 4

#  MERYL configuration
merylMemory   = 2000   # default 800MB
merylThreads  = 4      # default 1

# OVERLAPPER configuration
ovlOverlapper    = ovl      # default is ovl
merSize       = 14 # default is 22

utgErrorRate=0.03
utgErrorLimit=2.5  # Allow mismatches over and above the utgErrorRate. This helps with Illumina reads.
ovlErrorRate=0.05 # Larger than utg to allow for correction.
cnsErrorRate=0.06 # Larger than utg to avoid occasional consensus failures
cgwErrorRate=0.06 # Larger than utg to allow contig merges across high-error ends

gkpFixInsertSizes      = 1

doDeDuplication        = 1
doChimeraDetection     = normal

frgCorrConcurrency=4
ovlCorrConcurrency=4

unitigger     = bog
utgBubblePopping = 1
utgGenomeSize=1500000  # <- !!! I accidentally left this in from a different run

doResolveSurrogates=1
doToggle = 1
wichne 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 09:52 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO