Genomic assembly with spades

Question

[Buffo]

Hi everybody I`m using spades trying to assembly a trypanosomatid genome, i just have around 150 MB reads from nanopore sequencer, the smallest read its about 150 bp, and the longest about 84 kb, I know that i have no enough reads for genome assembly but I am trying to do it anyway, thats my command line:

spades.py --careful --nanopore --only-assembler -o out_spades -s file.fastq

It does not works, did somebody has used it before?

Thanks!

[Cliff Beall]

Maybe give the error message or describe how it fails?

[Buffo]

== Error == file not found: /home/fcallejas/bug4/mix_b4/--only-assembler (single reads, library number: 2, library type: nanopore)

[fanli.gcb]

Post your full command please. It looks like you either have typos or odd characters in your filename (so use quotes)

[Buffo]

spades.py --nanopore --only-assembler -o bug_spades -s mix_bug4.fastq

error message == Error == file not found: /home/fcallejas/bug4/mix_b4/--only-assembler (single reads, library number: 2, library type: nanopore)

i`m doing it by tcsh script on cluster.

Answer 1

[Cliff Beall]

Ok, actually it will only use Nanopore as part of a hybrid assembly. From the docs:

"SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available."

So it's expecting the nanopore reads filename after the --nanopore argument (which explains your error) but it's also expecting another file to do a hybrid assembly.

Do you have Illumina or other data?

[Buffo]

oh! that really has sense! and no, i have no other of reads for this assembly, i wil try it with celera or canu. Thanks!