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.