Question: Quality Trimming 454 Data - Software Recommendation
7
gravatar for Eric Normandeau
7.9 years ago by
Eric Normandeau9.9k
Quebec, Canada
Eric Normandeau9.9k wrote:

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!

ADD COMMENTlink modified 7.9 years ago by Ram0 • written 7.9 years ago by Eric Normandeau9.9k
9
gravatar for Rm
7.9 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

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
ADD COMMENTlink modified 7.9 years ago by Eric Normandeau9.9k • written 7.9 years ago by Rm7.8k

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

ADD REPLYlink written 7.9 years ago by Eric Normandeau9.9k
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