Calls to run Digital Normalization, Velvet and Oases

- Interleaving the paired-end files
% do-interleave.sh

- Install screed and khmer
% git clone git://github.com/ged-lab/screed.git
% git clone git://github.com/ged-lab/khmer.git

% cd screed
% python setup.py install

% cd khmer
% make test

% export PYTHONPATH=/root/khmer/python
% make KHMER=/usr/local/src/khmer

- Digital Normalization pass 1
% /root/khmer/scripts/normalize-by-median.py -C 20 -k 20 -N 4 -x 2.5e8 --savehash mk.kh paired_reads.fq.gz

- Digital Normalization pass 2
% /root/khmer/scripts/filter-abund.py mh.kh paired_reads.fq.gz.keep

- Digital Normalization pass 3
% /root/khmer/scripts/normalize-by-median.py -C 5 -k 20 -N 4 -x 1e8 paired_reads.fq.gz.keep.abundfilt

- Velvet is designed for DNA assembly. To assemble short reads from RNA, we need another program called Oases
- Install Velvet
% make 'MAXKMERLENGTH=49' 'OPENMP=2'
- Install Oases
make 'VELVET_DIR=/root/full_path' 'MAXKMERLENGTH=49'

- Assemble with Velvet

% velveth diginormassemble.33 33 -fasta -short paired_reads.fq.gz.keep.abundfilt.keep
% velvetg diginormassemble.33 -read_trkg yes -ins_length 328 -scaffolding no 

- Run Oases
% oases diginormassemble.33