This is a test version of Biostars. For the public version, visit https://www.biostars.org.
SPADES output

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.

contigs scaffolds output spades
• 1,357 views • link
written by san96 • san96

1 answer

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.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

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

• 0 views • link
written by san96 • san96

Log in to answer this question.

More posts like this