Entering edit mode
2.6 years ago
poecile.pal
▴
50
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