Script_for_denovo_s2

#!/bin/bash

#This is used in my docker container

##PATH
#DRAP install directory in the Docker container
cd /usr/local/src/drap

#DRAP configuration PATH
cd /usr/local/src/drap/cfg

#Edit configuration (change "local_cpu" and "n_cpu")
vi /usr/local/src/drap/cfg/drap.cfg

#Trimmed and filtered by Kraken2 sequence PATH
cd /mnt/data/pri_data/kraken

#DRAP working path
cd /mnt/data/out_drap_s2

##Step 1: merge forward and reverse reads (1 and 2), I use 15 cores here (-j15), you can change it based on your server
#remember to check the format of output, 
cd /mnt/data/pri_data/kraken && pwd && ls
cat *_1.fq.gz > merged_1.fq.gz
cat *_2.fq.gz > merged_2.fq.gz

##Step 2: run DRAP for denovo assembly
cd /usr/local/src/drap && pwd && ls

#Write script for further modification (change CPU number for faster speed if you want to, OPTION)
runDrap \
  --outdir /mnt/data/out_drap_s2 \
  --R1 /mnt/data/pri_data/kraken/merged_1.fq.gz \
  --R2 /mnt/data/pri_data/kraken/merged_2.fq.gz \
  --dbg trinity \
  --no-trim \
  --norm-mem 200 \
  --dbg-mem 200 \
  --discardN \
  --coverage 0,0.5,1 \
  --no-rate \
  --write

###ONLY DO THIS IF YOU RUN THIS FOR THE FIRST TIME###
#Edit the CPU number used in tgicl (It always fails when more than 6 CPUs are used here). This is a tool used in step 5. 
vi /usr/local/src/drap/bin/runAssembly.sh

# Change the second line into following command
tgicl all_dbg.fa -c 6 -l 60 -p 96 -s 100000
###


#runDrap (de novo assembly)
runDrap \
  --outdir /mnt/data/out_drap_s2 \
  --R1 /mnt/data/pri_data/kraken/merged_1.fq.gz \
  --R2 /mnt/data/pri_data/kraken/merged_2.fq.gz \
  --dbg trinity \
  --no-trim \
  --norm-mem 200 \
  --dbg-mem 200 \
  --discardN \
  --coverage 0,0.5,1 \
  --no-rate \
  --run

##Step 3: transcriptome quality assessment