Mosaik Aligning with 454 Reads

neolith · 01-05-2010, 06:19 PM

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 · 01-06-2010, 06:25 PM

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....

donniemarco · 07-21-2010, 12:52 PM

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.
Thanks!!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
aligning the reads	kjaja	Bioinformatics	2	07-07-2019 07:45 AM
Using Mosaik to assemble bacterial genome 454 sequencing	jpearl01	Bioinformatics	2	03-27-2013 07:29 AM
Mosaik Aligning with Solexa Reads	JimC	Bioinformatics	5	06-06-2012 06:07 PM
bwasw scoring parameters when aligning 454 RNA-seq reads on the human genome	dgacquer	Bioinformatics	0	09-02-2010 06:24 AM
454 mate pairs and mosaik	afb	Bioinformatics	4	04-02-2010 06:07 AM

01-05-2010, 06:19 PM	#1
neolith Junior Member Location: Seoul, Korea Join Date: May 2009 Posts: 3	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...

01-06-2010, 06:25 PM	#2
neolith Junior Member 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....

07-21-2010, 12:52 PM	#3
donniemarco Member 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. Thanks!!