Quality Trimming 454 Data - Software Recommendation

Question

[Eric Normandeau]

Hi,

I am looking for a powerful and flexible tool to trim 454 sequences. I would like it to be able to remove the following:

• Tags
• 454 adaptors
• Low complexity regions
• Poly-A/T
• Low quality regions

The sequences can be either in .sff or .fasta/.qual format.

I'm keen on knowing what you guys would recommend and why :)

Cheers!

Answer 1

[Rm]

Try NGS_Backbone: It can clean sanger, 454 and illumina sequences.

http://bioinf.comav.upv.es/ngs_backbone/cleaning.html#clean-reads

and also "FASTX-Toolkit"

For Illumina data. I use fastx toolkit to do some of the above analysis which you are looking.

For example

Quality filter at Q 12 and atleast 50% good bases and End trimming with quality filter at 12 and minimum length (30 bases) of the read to retain the read.

fastq_quality_filter -q 12 -p 50 -i Input_reads.txt | fastq_quality_trimmer\
    -t 12 -l 30 -o filtered_reads.out.txt

my barcodes are 8-bases long

cat filtered_reads.out.txt | fastx_barcode_splitter.pl --bcfile mybarcodes.txt\
    --bol --exact --prefix filtered_reads.out.txt.

fastx_trimmer -f 9 -i filtered_reads.out.txt.Tag1 \
    >filtered_reads.out.txt.Tag1.txt

[Eric Normandeau]

Thank you RaghuM :) I'll dig into FASTX-Toolkit more seriously!