rnaSPAdes hybrid assembly with YAML file

[poecile-palustris]

Good morning,

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

[asl]

Hello

No need to specify --nanopore as you have already specified the type of the library in the YAML, so it is redundant.

[poecile-palustris]

Anton, thank you very much for the fast answer!