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Old 01-05-2010, 05:19 PM   #1
Junior Member
Location: Seoul, Korea

Join Date: May 2009
Posts: 3
Unhappy Mosaik Aligning with 454 Reads

How long will it take to finish the Mosaik Aligning work?

In the manual for Mosaik1.0, MosaikAligner aligned the lane of 6,563,762 Illumina paired-end reads(36bp) in 45.9minutes (2,390 paired-end reads/s) to the entire human genome(2.9Gbp) using 8processor cores.

And in the manual for Mosaik, Aligner setting for 454 GS-FLX : -hs 15 -mm 0.05 -act 26

But in the case of version 0.9.891, the lane of 119,263 '454 reads'
expected time of alignment over 50 hours.(0.6 reads/s)

Used commands are :
MosaikAligner -in input.dat -out aligned.dat -ia total.ref.dat -hs 15 -mm 0.05 -act 26 -m all -mhp 100 -j h.sapiens_15 -p 8

Mosaik version : 0.9.891-linux-x64

I will do the job with version 1.0.1367, and I want to reduce working hour...
neolith is offline   Reply With Quote
Old 01-06-2010, 05:25 PM   #2
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Location: Seoul, Korea

Join Date: May 2009
Posts: 3

In the case of Mosaik version 1.0.1367,
aligned the lane of 119,263 '454 reads', in 246minutes (7.7 reads/s)
to the entire human genome(3.0Gbp) using 8 processor cores....
neolith is offline   Reply With Quote
Old 07-21-2010, 11:52 AM   #3
Location: USA

Join Date: Aug 2009
Posts: 17

How can I create one single dat example total.ref.dat for the entire genome. The data available are in seperate files for each chromosome.
I want to run entire index data with mosaik for all the chromosome together.
donniemarco is offline   Reply With Quote

454, mosaik, mosaikaligner

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