genomic analysis workflow for plants

Question

[StudentBio]

please can someone share with us ta link where can i find the workflow för genomic analysis..... for assembly

fastq file, single end, ion torrent, palm plant genome

[lieven.sterck]

you might want to be a little more specific in your question?

what species? what kind of input data? ...

[StudentBio]

palm plant fastq file single end fron ion torrent

[h.mon]

What is the expected genome size and ploidy? What is the targeted coverage?

I've seen MIRA and SPAdes cited as tools used for Ion Torrent assembly, but never for plants - both tools are developed for small- or medium-sized genomes. If you can get a copy of Newbler, it will probably work well for Ion Torrent data.

Answer 1

[colindaven]

Single ended FASTQ files only are going to work very badly for a plant genome which is likely large and repetitive. If a reference genome is available I would do alignments instead.

If you have to assemble contigs, you might try Soapdenovo2, but I would not expect much. Also Ion Torrent has lots of indel errors - causing false positive frameshifts in ORFs - so is a very poor choice.