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SPAdes output strange with list of kmers as input

Here is an example command I ran:

spades.py -k 25,27,39,47,53,55 --careful -o Output_Directory -1 file1.fastq -2 file2.fastq -s single.fastq

The output is: Output_Directory ->

Output Directory

then inside each of the K__ folders ->

screenshot2

I expect to see a scaffolds.fasta and scaffolds.fastg file in each of the K__ folders, and while some have them, most do not. Additionally, some of the Output_Directories have a scaffolds.fasta file. Why are there contig and scaffold files that are NOT in the specific Kmer folders? I'm really at a loss, the manual was not helpful.

assembly
• 368 views • link
updated by Ram Ram • written by steven steven

Did you look at spades.log and warnings.log? Anyway, I sometimes had problems when manually setting kmers, did you try -k auto, or picking less kmers?

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updated by Ram Ram • written by h.mon h.mon

1 answer

Well I feel like an idiot now. I just read the SPAdes paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/ and from the introduction:

SPAdes is a universal A-Bruijn assembler in the sense that it uses k-mers only for building the initial de Bruijn graph and "forgets" about them afterwards; on subsequent stages it only performs graph-theoretical operations on graphs that need not be labeled by k-mers. The operations are based on graph topology, coverage, and sequence lengths, but not the sequences themselves. At the last stage, the consensus DNA sequence is restored.

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updated by Ram Ram • written by steven steven

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