3. Run Spades

3. Run spades - it takes a long long loooong time

while read f; do spades.py -k 21,33,55,77 --careful -1 "$f"_forward_paired.fq.gz -2 "$f"_reverse_paired.fq.gz -s "$f"_forward_unpaired.fq.gz -o "$f"/ -t 56 -m 416; done < acc1234

Following manual at <http://spades.bioinf.spbau.ru/release3.10.1/manual.html>

Specific for multi-cell data set with read lenght 2x150, using SPades error correction BayesHammer module.

From Fev 18th 18:22h to Fev 20th 23:16h for 40 samples on tobyG1.