Error correcting Ion Torrent data

[jagos01]

I would like use Unicycler for hybrid assembly of Ion Torrent and nanopore data. The default assembly option in Spades is not appropriate for Ion Torrent error correction/assembly. Ion Torrent data requires the --iontorrent flag to be used. Is it possible to add this as an argument for Unicycler?
I tried using Spades with the --only-error-correction flag to generate error corrected reads that could be used with Unicycler. The problem is ionhammer (the error correction module used with the --iontorrrent flag), outputs the sequences as a seq.fa.gz not seq.fq.gz which is required for Unicycler. Is there anyway to use the --iontorrent flag with Unicycler? Thanks, Scott

[tigerxu]

Hi Scott,

I have a same question. I have Ion Torrent and Pacbio data. Have you solved this issue? Any suggestion is very appreciated! Thanks, Zhuofei

[jagos01]

Hello Zhuofei, I error corrected the Ion Torrent data using spades (--iontorrrent and --only-error-correction flags) and then converted the fasta file to fastq with the attached script (use script at your own risk). Hope this helps, Scott

On Sun, Dec 1, 2019 at 9:28 PM tigerxu notifications@github.com wrote:

Hi Scott,

I have a same question. I have Ion Torrent and Pacbio data. Have you solved this issue? Any suggestion is very appreciated! Thanks, Zhuofei

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[tigerxu]

Hi Scott, I see, thank you very muh for your help! Zhuofei

[tigerxu]

Hi Scott,

I didn't find the attached script you mentioned above to convert the fasta to fastq file. Could you help to attach it again?

Thanks a million! Zhuofei

[jagos01]

Hello Zhuofei, Sorry for the late reply. Here is a link to the script I used for the conversion (fasta_to_fastq.pl).
https://code.google.com/archive/p/fasta-to-fastq/ Scott

[tigerxu]

Hi Scott, Thanks very much for your help! Zhuofei

[mradz19]

@jagos01 Hi Scott,

I too am attempting a hyrbid assembly with iontorrent and nanopore reads. Just to confirm did you use spades to error correct the nanopore reads with the ion torresnt reads, then use that output for unicycler assembly with specifying to skip error correction?

[jagos01]

Hello mradz19, I only used spades to correct the ion torrent data. I then did a hybrid assembly with unicycler using spades corrected ion torrent reads and raw nanopore reads.