SPAdes: with different read length

[bio_informatics]

Hi members,

I'm facing something weird. I know not all reads in the fastq files can have same length.
But in my trimmed data, read length of reverse and forward files are different. I checked out for only first read, though.

Data: paired end
Organism: E. coli

Output 101 from reverse strand:

zcat sample_R2_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}'  | head -1

Output 54 from forward strand:

zcat sample_R1_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}'  | head -1

An icing to this dilemma is, SPAdes uses 55 as K-mer during assembly. And the genome size from assembly is reasonable.

My questions:

1) Shouldn't SPAdes select K-mer less than 55 here?

[GenoMax]

Can you tell us why are they different (and uniformly of length 54 for R1)? Did you trim them that way?

[bio_informatics]

Hi Genomax,
Thanks for your reply.

I've 2 sets of data, trimmed (sequencing center did this trimming based on the quality)and untrimmed. I used the already trimmed data for assembly.

Oh, they aren't uniform ( looking at already trimmed file).
Have 72 different lengths: max is 101, minimum 30.
So, in a way, all numbers from 30-101 are present for read lengths. That's strange. :-/

[GenoMax]

In that case your original question is no longer applicable, correct?

[bio_informatics]

Yes.
Sorry.

In that case your original question is no longer applicable, correct?

[GenoMax]

No problem. Sounds like you did get a reasonable sized assembly so all should be well.

[bio_informatics]

Yes, that is more important.
Merci!