A tool to cut off a certain length of nucleotide from reads

Question

[s.kyungyong64]

Hi,

I have a genome of plant provided by a lab for me to assemble. This genome has Pac Bio and Illumina primer sequences that need to be removed beforehand. But I was told that some of the primers do not retain their full sequences, so instead of looking for the full sequences and trimming them out using software, they simply remove 70(?) nucleotide from both ends of every reads. Is this a better approach? And what tool would allow me to do this?

Thanks!

[shenwei356]

Question: Trimming of partial adaptor sequences

Answer 1

[cschu181]

In before Brian Bushnell suggests BBDuk. Use BBDuk: http://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/ >:D

[Brian Bushnell]

Oh, and I was so close, too!

[s.kyungyong64]

Thank you! It's time to get back to bbduk then!

Answer 2

[Brian Bushnell]

At least for Illumina reads, that's a bad idea. Especially for libraries under 140 bp, since you'd have nothing left (but assembly would run very fast!)

PacBio libraries don't have read-end adapters like Illumina. Rather, they have "Smart Bell" adapters somewhere in the middle of the read. PacBio's software already removes those for you when creating filtered subreads. Sometimes it doesn't get all of them, so I wrote a tool to remove them removesmartbell.sh), but it's not normally necessary. Therefore for PacBio my recommendation is: Do nothing, though you can try running removesmartbell.sh if you are feeling adventurous or are interested in knowing whether there are any leftover adapter sequences.

For Illumina, you should do adapter-trimming as indicated here. You can also use BBDuk to forcibly trim the first and last 70bp from every read, but I don't recommend that in this case.

[s.kyungyong64]

Thank you for your helpful answer! I will follow your suggestion!