Use Illumina mate pair and paired ends with novoalign

[k2bhide]

Hello all,

I have 3 sets of Illumina mate pair sequences and 2 sets of Illumina paired end sequences with different insert sizes each. I need to align all the reads simultaneously to reference genome using novoalign.

Could you please let me know how can I modify the novoalign command in order to include all the read sequences to align at once against the reference genome.

Any help is this regard will be appreciated.

Regards

Ketaki Bhide

[zee]

Hi Ketaki,

Your task is is best accomplished by launching separate novoalign commands for mate-pair and paired end.

Considering the case where your paired-end fragment lenghts are 300bp with standard deviation=100 we map using the following command:

novoalign -d database.nix -f read1.fastq.gz readd2.fastq.gz -i 300 100


In the case of mate pairs where distance between 2 mates is 2000bp (SD=200), then we do

novoalign -d database.nix -f read1.fastq.gz readd2.fastq.gz -*i MP 2000,200


You can map gzip compressed files directly. Please go to our website at www.novocraft.com and request a license key to unlock all these extra features for your work.