SAM File to Abyss-fixmate?

[Febri Gunawan]

I read that Abyss can make SAM File but the sequence and quality is printed as "*". So I have to use abyss-fixmate. Now, I want to ask two questions:
1. I read that usage of abyss-map is abyss-map [option] query target so what is the query and target? no spesific explanation. So, I use fastq file as query and xyz-contigs.fa as target, am I right?

2. How to use abyss-fixmate? I use this command:
abyss-fixmate -h coverage.hist abc.sam > fgh.sam, but the result is mateless.


Thank you,
Best regards

Febri

[Tony Raymond]

Hi Febri,

Query are the sequences you want to align (usually reads). Target is the thing you are aligning to (usually reference or assembly).

In the latest version of ABySS we compile two different executables to keep/remove the sequence and quality strings. If you want to keep the sequences, you need to use the executables with the "-ssq" suffix. So here you would use abyss-map-ssq and abyss-fixmate-ssq. We needed to compile difference executables for this for performance reasons.

For abyss-fixmate, don't specify the histogram file if you are trying to get just the alignments. Try this:

abyss-fixmate-ssq -v abc.sam > fgh.sam

Cheers,

Tony

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