Basic questions about SPAdes, metaSPAdes

Question

[yingcraft]

I am a new student of bioinformatics. Now I have clean nanopore sequencing reads data A and B (bacteria), I want to assemble each reads to contigs and compare the difference. I try to use the code : spades.py -nanopore A.fastq.gz B.fastq.gz -o result But the terminal reported error. I 'm not sure whether it is the problem that the SPAdes can't assemble the nanopore reads without illumina data. Can you explain the reason and give me some advice, please? Thanks!

[andres.firrincieli]

hello,

please report the error message next time.

I 'm not sure whether it is the problem that the SPAdes can't assemble the nanopore reads without illumina data. Can you explain the reason and give me some advice, please? Thanks!

Pretty sure that spades was designed as hybrid assembler, so it requires Illumina reads. In general, for Nanopore sequencing data there are better options out there, like Canu or Flye. Since you have metagenomic data, you should go for metaFlye.

Answer 1

[yingcraft]

Thanks for your advice! I will try metaFlye.