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====== ASSEMBLING LONG READ DATA ======

When you have your porechopped reads in fastq and fasta formats, try out the following assemblers:

Programs: ABruijn ([[https://github.com/fenderglass/ABruijn]]), Canu ([[http://canu.readthedocs.io/en/latest/quick-start.html]]), smartdenovo ([[https://github.com/ruanjue/smartdenovo]]), miniasm ([[https://github.com/lh3/miniasm]])

**ABruijn**
ABruijn is relatively simple to use. As its name suggests, it uses A-Bruijn graph to find the overlaps between reads. It has a polishing step to improve quality.

It needs a fasta input. The final product is a polished_(1+number of iterations specified).fasta.
<code>
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -cwd
#$ -pe threaded 10

unset PYTHONPATH
export PATH=/scratch2/software/Python-2.7.13/bin:$PATH
export LD_LIBRARY_PATH=/scratch2/software/Python-2.7.13/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/scratch2/software/hdf5-1.8.18/lib:$LD_LIBRARY_PATH
export PATH=/scratch2/software/blasr/bin:$PATH

cd /path/to your working directory

/scratch2/software/ABruijn-1.0/bin/abruijn /path/to_your_fasta /path/to_an_output_directory <estimated coverage> --platform nano --threads 10
</code>
**Canu**

**smartdenovo**

**miniasm**

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