SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Computer Language Benchmarks Game gringer Bioinformatics 0 12-12-2011 02:29 PM
Very Bad Mapping Results with several mapping softwares xquan Bioinformatics 13 05-22-2011 11:31 PM
PubMed: Optical mapping of DNA: Single-molecule-based methods for mapping genomes. Newsbot! Literature Watch 0 01-06-2011 02:00 AM
Why do we use mapping programs instead of blast for mapping to a reference? thsuk1 Bioinformatics 6 08-27-2010 08:54 AM
Maq mapping score and "Mapping uniquely"?? sdwy2008 Bioinformatics 0 06-03-2010 08:53 AM

Reply
 
Thread Tools
Old 08-08-2008, 09:37 AM   #1
kmay
Member
 
Location: Munich, Germany

Join Date: Aug 2008
Posts: 29
Cool Mapping benchmarks of the GMS

Hi,

As I promised in another thread here some first controlled benchmarks from the Genomatix Mapping Station ( GMS):
  • Random pick of 1Mio reads (32bps) across the human genome (NCBI build 36)
  • Generate 1bps insertions and 1bps deletions in 1% of the reads
  • Generate 1 bps substitutions in 10% of the reads

Mapping time: 375 seconds

Correctly identified reads: 921.799 (92 %)
Found perfect alignment for read with indel: 2.653 (0.2%)
Ignored because ambiguous: 43.057 (4%)

=====================================
Real life data:

Illumina: ChipSeq STAT1 human
Total: 5.069.935 reads
Length of reads: 36

Time: 1.524 sec (about 5 min per 1.000.000 reads)

Result:
4.150.890 unique best hits (81 %)
3.151.593 with alignment score > 0.9
207.636 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
560.920 reads with multiple best hits

====================================
Real life data:

Helicos DGE human tissue

Total: 4.397.276 reads
Length of reads: 5bps to 140bps

Time: 527 sec

Result:
1.662.837 sequences were ignored (too small) (37 %)
2.011.375 unique best hits (45 %)
777.434 with alignment score > 0.9
665.631 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
723.064 reads with multiple best hits
kmay is offline   Reply With Quote
Old 08-09-2008, 04:35 AM   #2
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

This looks good.

What Hardware conditions e.g. RAM, CPU clock speed, etc are these benchmarks running on?
zee is offline   Reply With Quote
Old 08-09-2008, 06:27 AM   #3
Chipper
Senior Member
 
Location: Sweden

Join Date: Mar 2008
Posts: 324
Default

How does it compare to the Eland alignments (e.g. # aligned sequences etc) for STAT1? Was the DGE alignments done with or without splice junctions?
Chipper is offline   Reply With Quote
Old 08-09-2008, 09:59 AM   #4
kmay
Member
 
Location: Munich, Germany

Join Date: Aug 2008
Posts: 29
Default

Hi,

no fancy hardware, just an opteron processor, 2GHz
but 64GB of main memory!

->Chipper: I am travelling in the US this week. IŽll try to give you some answers later, or ask a colleague to jump in.

Klaus
kmay is offline   Reply With Quote
Old 08-11-2008, 03:05 AM   #5
clivey
Member
 
Location: Oxford

Join Date: Jul 2008
Posts: 24
Default

Eland was designed to avoid having 64Gb of memory. It should do about 4000 reads per second per CPU on a modern CPU so ~250 seconds.
clivey 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 06:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO