Assembly Tools With Fastq File As Input

Question

[Pdubois]

Dear expert,

Is there any program that uses quality score in the method? (i.e. uses FASTQ file as input).

-Peverall

[Michael Schubert]

Sine you tagged your question Solexa, I assume you are using Illumina sequencing. Setting aside whether you actually need quality scores (as Velvet seems to be the first choice in that case), take a look at MIRA.

[Ryan Thompson]

FASTQ is not the only sequence format that includes quality information. It seems like you are really asking for an assembler that uses quality scores.

Answer 1

[Michael Schubert]

Since you tagged your question Solexa, I assume you are using Illumina sequencing. Setting aside whether you actually need quality scores (as Velvet seems to be the first choice in that case), take a look at MIRA.

Note that quality scores are not as important in short-read assembly as they are in e.g. Sanger sequencing, as they can often be inferred from coverage alone. Assemblers that do take these scores into account have so far not significantly outperformed those that do not (source for QSRA here).

Some newer assemblers that you might want to look at as well are EDENA or IDBA that (as far as I know) do neither account for quality scores as well.

(this is in part copy-paste from the comment)

[Bach]

Depending on the use case, quality data may still be quite important. Finding rare SNPs in RNASeq comes to mind, where looking just at the coverage of possible variants will yield high numbers of false positives. Slashing that number by a factor of 2 to 10 might make the difference between being able to to follow-up experiments or not.