Whole genome assembly of Ion torrent single-end data

Question

[mittu1602]

Hello all,

My goal is to do whole genome assembly of a fungal taxonomy, I have fastq file reads that are from Ion torrent platform, the data is single-end reads, I also have a reference genome. I already tried using tools like AByss, and MIRA. The problem with these two tools are too many contigs file and repeat contigs respectively. I am looking for correcting the contigs file or a good assembler tool which is easy to install and understand. Also if there is a solution for correcting the contig file, How do I lead to scaffold stage?

I read some threads on the similar type of posts which used newbler tool but newbler links are no longer available also the input needed is SFF file format which is also not available for me. Any kind of help would be appreciated.

Thank you!

Answer 1

[5heikki]

SPAdes works best with bam files straight out of PMG. Good start would be: --iontorrent -k 21,33,55,77,99,127 --careful

This generally results in ca. 100 contigs, which is pretty decent for bacterial genomes. You can't have much better than that with short reads. This is good enough for RefSeq Genomes and gives you e.g. 99.9% complete proteome..

[mittu1602]

Thank you, but my fungi genome is an eukaryote will it still work?