8.6 years ago by
Try NGS_Backbone: It can clean sanger, 454 and illumina sequences.
and also "FASTX-Toolkit"
For Illumina data. I use fastx toolkit to do some of the above analysis which you are looking.
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 \