mate pair trimming ?

Question

[Picasa]

Prior to an assembly, I would like to trim out adaptor sequences from mate pair library.

I use usally Trimmomatic, but it doesn't suit for mate pair because of orientation right ? Do you have any recommandation for mate pair trimming ?

[DVA]

You can try Cutadapt. More information can be found: Trimming Adapters

Answer 1

[Antonio R. Franco]

Take a look to BBDuk. There is plenty of information about it HERE

Answer 2

[Shicheng Guo]

You can try Trim_galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/:

Single end

trim_galore $phred --fastqc --illumina --clip_R1 3 --clip_R2 3 $read[0] --output_dir ../fastq_trim

Pair-end

trim_galore $phred --fastqc --illumina --paired --clip_R1 3 --clip_R2 3 --three_prime_clip_R1 3 --three_prime_clip_R2 3 $read[0] $read[1] --output_dir ../

Answer 3

[Chris Fields]

If you are removing the Nextera internal adapter for mate-pair libraries, you should use NxTrim:

https://github.com/sequencing/NxTrim

This will both trim the internal adapter and categorize the reads into groups: true mate-pairs, single-end, paired-end, and unknown (no adapter found, so likely a mix of true mates and paired-end). Note that the tool will revcomp the output by default to make them innies, which is NOT what most assemblers want. You can stifle this to keep the outie orientation by using the --norc option.

Otherwise, the above choices will work for other standard adapter sequences.

[Picasa]

I' want to try this soft with a mate pair library (insert length of 3000). So what is the differentce between theyr true mate and their paired end ? is the paired end still have an insert length of 3000 ?.

Does is trim sequencign adaptor too ? (like P1 etc.)