Assembling Short Sequence

Question

[joseph.landry]

Hi Everyone,

I am sequencing 250 bp PCR fragments using paired end 150bp illumina sequencing. The sequence in read 1 and read 2 will allow me to assemble the complete sequence of each 250 bp fragment (150 in one direction and 150 in the reverse). I just need to take the reverse complement of read 2 then trim the overlapping sequence from read 1 and then concatenate them. How do I do that for 10+ million fragments? I can use the command line and most common sequence processing software (bedtools, etc...). Any suggestions would help me greatly.

Thanks

JL

Answer 1

[h.mon]

Any read merging software will do what you want. I suggest BBMerge from the BBTools package. Other options are FLASH, PEAR, VSEARCH, among others.