Error with metagenome assembly using nanopore library

ablab / spades

SPAdes Genome Assembler

http://ablab.github.io/spades/

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Error with metagenome assembly using nanopore library #421

Closed nsng closed 4 years ago

nsng commented 4 years ago

Hi there,

I have a single library sequenced with nanopore and I am trying to perform a metagenome assembly. I've tried running the command below but I keep getting the following error.

spades.py --meta --nanopore -s porechop_ter_mats.fastq -o spades_ter_mats

== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: porechop_ter_mats.fastq

asl commented 4 years ago

Hello

SPAdes manual (http://cab.spbu.ru/files/release3.14.0/manual.html#sec3.1) reads:

Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.