rnaSPAdes hybrid assembly and YAML file

Question

[poecile.pal]

Good evening,

I would like to make a hybrid assembly (Illumina + Oxford Nanopore) using rnaSPAdes. I have a lot of libraries, so I have to set them in a YAML file. Do I understand correctly that in this case I need to specify both those and other libraries in YAML, and write the code as follows:

rnaspades.py --dataset libraries.yaml --nanopore -o OUTPUT

(without specifying anything after --nanopore)

with YAML like this:

 [
      {
        orientation: "fr",
        type: "paired-end",
        right reads: [
          "/FULL_PATH_TO_DATASET/lib_pe1_right_1.fastq",
          "/FULL_PATH_TO_DATASET/lib_pe1_right_2.fastq" 
        ],
        left reads: [
          "/FULL_PATH_TO_DATASET/lib_pe1_left_1.fastq",
          "/FULL_PATH_TO_DATASET/lib_pe1_left_2.fastq" 
        ]
      },
      {
        type: "nanopore",
        single reads: [
          "/FULL_PATH_TO_DATASET/nanopore_1.fastq" 
          "/FULL_PATH_TO_DATASET/nanopore_2.fastq" 
        ]
      }
 ]

Thank you in advance!

Best regards, Poecile

Answer 1

[poecile.pal]

I duplicated my question on github and the developer answered that specifying --nanopore is not required in this case, since it is already specified in YAML. So:

rnaspades.py --dataset libraries.yaml -o OUTPUT