Alignment Software That Considers Fastq Quality

Question

[Love]

We know that the Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. But it seems that it doesn't have quality of fastq. So what is the best software to deal with it?

I want to compare two sequence with fastq quality such as

GCCTACAGAATCTAGAAAATAgcctcaaaaggacaaatctaagtggtattggccttaaag
aggaggtggggagtgtagaaagtgtattcaaagggatagtaacagaacgtcccaaaccta
cagaaagatatcaatatccaagtacaagaaagttataaaacaccgagcagatgtaactca
aagaagactacctcaaggaatttaataatcacagtcccaaagatcaaggataaagaaagg
atcttaaaagcagcaagagaaaagaaaccaataatatacaatggagctacaatatatctg

And

ACCATGCTGTTTTGGATACTGTAGCCTTATAGTTTGAAGCCTCTGGCTTTGCCCTTTTGC
TTAGATTTGCTTAGGCTGTTGAGGCCCTCTTTTGGTTTCATATGACTTCTagaatacttt
tttctaattctgtgaagaacgaCATTGGTAGTTTGATAGAAATAGCACTGAATCTGTCAA
TTGCTTTGGGCAGTGTGGCCATTTGAATGATACtgattcttccaatccatgagcatggaa
tgtttttccatttaattgtgttatctctgatttctttccgcagtgttttatagttcttgt

Not sure if it is a proper question.

Thanks.

[Casey Bergman]

I don't understand how quality is being represented here - are you trying to depict quality as lowercase or blue or are you interested in using a true fastq file format?

[Love]

I am just interested in using a true fastq format. I am not sure why the blue was printed after I copyied and pasted strings.

Answer 1

[Jeremy Leipzig]

Most people just trim, but there is something to be said for quality scaling. Ketil Malde's paper "The effect of sequence quality on sequence alignment" discusses this.

http://bioinformatics.oxfordjournals.org/content/24/7/897.short

The pairwise alignment tool in Biostrings has some facilities to deal with this as well.

[Love]

How to trim it? Do you mean to use "FASTX" toolkit?

[Jeremy Leipzig]

yes either fastx or sickle or using a bio* project

[Love]

I am going to use fastx, so which command should I use? FASTQ Quality Filter? or FASTA/Q Trimmer? There are many "n" in the sequence, should I discard it?