This is my first time to assemble long reads from nanopore sequencing. I also have the short reads generated by Illumina sequencer. Here is my plan, to use wtdbg2 to get the draft genome fasta file, then to use pilon to polish. However, I have been blocked at the getting-started part of wtdbg2. I am totally confused by the input and output files in the following command lines. Are they just in one pipeline or just independent examples?
#quick start with wtdbg2.pl ./wtdbg2.pl -t 16 -x rs -g 4.6m -o dbg reads.fa.gz # Step by step commandlines # assemble long reads ./wtdbg2 -x rs -g 4.6m -i reads.fa.gz -t 16 -fo dbg # derive consensus ./wtpoa-cns -t 16 -i dbg.ctg.lay.gz -fo dbg.raw.fa