Hybrid Assembly From Illumina and Ion Torrent Reads

Question

[Optimist]

Hello Everyone,

Greetings!!

I have sequencing reads of a Bacterial strain from Ion Torrent PGM (Unpaired; Single) and Illumina (Paired Reads) platforms. Can you please let me the tool used for the Hybrid assembly using reads from both the platforms. What are the parameters to be used in the tool to generate a good assembled genome.

Thanks a ton

Regards

Optimist

[Optimist]

Learnt that SPAdes v3.13.1 is one of the tools used for Hybrid Assembly. Kindly do let me know if there are any other tools that serve the purpose.

Thank You

Answer 1

[hugo.avila]

Hi ! Do try spades it is a very good assembler and it can support two reads datasets from different sequencing technologies. I have never tried assemble illumina and Ion together but i think it will work, at least the documentation did not state otherwise. The command line will need some careful reading of the spades documentation because it is good to optimize the parameters to fit your needs (here is a quick guide). Try this to start:

spades.py -1 forward_illumina_reads.fastq -2 reverse_illumina_reads.fastq --iontorrent -s ion_torrent_reads.fastq -o spades_output

Do try more parameters like --careful and different k-mer sizes with -K, also optimize your computer resources like cpu -t and RAM -m.