Both long and short read of the same sample

Question

[angela.tithi23]

For an experiment, we need both short and long read sequences of the same sample. Is there any website that provides both the pacbio/nanopore and illumina reads? (We will construct de novo assemblies with them further.) We do not need samples that have larger genomes, within 5.0 million bp size will do. Thank you!

[GenoMax]

You will need to search on SRA to see if you can find such datasets. Use SRA-explorer.

A previous thread had addressed this for RNAseq data: Question about downloading RNA-seq long reads and short reads for the same sample

[angela.tithi23]

Thank you so much! I got a paper and got the accession numbers! ^_^

[WouterDeCoster]

The most straightforward way is probably to search for a paper which did a hybrid assembly for some big genome, plenty of recent examples.

[angela.tithi23]

Thank you so so much! It helped! I got a paper where the accession numbers are well organized! Thank you again! ^_^

[Friederike]

It might be helpful to know what you plan on doing with those reads.

[angela.tithi23]

I am gonna make de novo assemblies with that. :)

Answer 1

[swbarnes2]

Unicyler on Galaxy might do what you want

https://usegalaxy.org/

[angela.tithi23]

Thank you so much, but I may have written the question in a wrong way. Unicycler is a hybrid assembly pipeline, na? But I need the reads, not the assembler. I am sorry, I am correcting the question. :( If you know a website that provides both pacbio/nanopore and ilumina reads, please let me know. Thanks once again!