SPADES output

Question

[sansan96]

Hello,

I just assembled a fungal genome with SPADES and I have a question about which output file to take. In the output I have a file of contigs and another of scaffolds, which will be ideal for subsequent analyses?

I also see that they have some difference in the number.:

[user@server assembly_T9_kmer]$ grep -c ">" contigs.fasta
222
[user@server assembly_T9_kmer]$ grep -c ">" scaffolds.fasta
194

My script:

spades.py -o assembly_kmer -1 T6_S49_P_R1.fastq.gz -2 T6_S49_P_R2.fastq.gz -k 21,33,55,77,99,127

Thanks so much.

Answer 1

[Mensur Dlakic]

If memory serves well, SPADES will attempt to join some scaffolds into contigs when there is enough evidence that contigs are connected but not enough difference for the exact sequence. In a scaffold file there will be some sequences joined with a string of Ns. If your goal is to have the highest quality sequence, you should go with contigs.fasta. In the other file there will me slightly more sequence but all those extra sequence pieces will be Ns. However, scaffolds.fasta will be less fragmented if that makes a difference for you.

[sansan96]

Thanks so much for your answer, I will take contigs.fasta.