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Running-PBJelly-example-with-indel-correction-with-BBMap-no-Pilon
# goes along with http://seqanswers.com/forums/showthread.php?p=220925#post220925
#
# assumes you have PBJelly, blasr, tabix, bcftools, samtools installed
# below I am using a machine with 70 cores on a single node, adjust to the number of cores to your machine
# The scripts below are obviously not designed for use with a cluster, but can be modified
#
#########################
# STEP 1 Combine the FASTQ files and remove the originals to save space
#########################
## first combine files and delete the originals to save space
WorkDir=/genetics/elbers/pacbio
cd ${WorkDir}
cat ?.subreads.fastq > pacbio-genome-pbjelly.fastq
rm ?.subreads.fastq
## second add fake quality values (from Q0=! to Q30=> in Sanger encoding) for pbjelly to work
cat pacbio-genome-pbjelly.fastq | tr "!" ">" > pacbio-genome-pbjelly-fqual.fastq
#########################
# STEP 2 Create pbjelly-config-assemble.xml
#########################
## use nano to create the file then paste everything between the lines starting with #### and ending with ####
nano pbjelly-config-assemble.xml
####pbjelly-config-assemble.xml####
<jellyProtocol>
<reference>/genetics/pacbio/genome.fasta</reference>
<outputDir>/genetics/pacbio/</outputDir>
<cluster>
<command notes="For single node, multi-core machines" >${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &amp;</command>
<nJobs>70</nJobs>
</cluster>
<blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 10 -maxScore -500 -nproc 1 -noSplitSubreads</blasr>
<input baseDir="/genetics/pacbio/">
<job>pacbio-genome-pbjelly-fqual.fastq</job>
</input>
</jellyProtocol>
####pbjelly-config-assemble.xml####
#########################
# STEP 3 Create fake qualities for reference to fill in gaps for
#########################
/opt/PBSuite_15.8.24/bin/fakeQuals.py genome.fasta genome.qual
#########################
# STEP 4 Summarize the assembly and reads
#########################
## first Summarize the assembly
/opt/PBSuite_15.8.24/bin/summarizeAssembly.py genome.fasta > genome.fasta.summary
## second Summarize the reads
/opt/PBSuite_15.8.24/bin/readSummary.py pbjelly-config-assemble.xml > pacbio-genome-pbjelly-fqual.fastq.summary
#########################
# STEP 5 Setup pbjelly
#########################
## note - this step takes about 1 hour
## note2 - pbjelly steps are submitted in the background, but even though it says step is
## finished, it might not be, you need to see if there are still pbjelly processes running
## for example "ps aux|grep -v "root"|less -S" to see if you still see PBJellySuite or
## blasr or Setup.py or Extraction.py or Support.py or Assemble.py or Out.py
/opt/PBSuite_15.8.24/bin/Jelly.py setup pbjelly-config-assemble.xml
#########################
# STEP 6 Map FASTQ reads to genome.fasta reference
#########################
/opt/PBSuite_15.8.24/bin/Jelly.py mapping pbjelly-config-mapping.xml
#########################
# STEP 7 Summarize mapping results
#########################
/opt/PBSuite_15.8.24/bin/Jelly.py support pbjelly-config-assemble.xml -x "--minMapq=50"
#########################
# STEP 8 Extract reads that appear to bridge gaps
#########################
/opt/PBSuite_15.8.24/bin/Jelly.py extraction pbjelly-config-assemble.xml
#########################
# STEP 9 Assemble reads to fill in gaps
#########################
/opt/PBSuite_15.8.24/bin/Jelly.py assembly pbjelly-config-assemble.xml
#########################
# STEP 10 Produce output with gaps filled in
#########################
/opt/PBSuite_15.8.24/bin/Jelly.py output pbjelly-config-assemble.xml
#########################
# STEP 11 Convert het bases to hom and convert lower to uppercase
#########################
## see https://github.com/lh3/seqtk for a link to download seqtk
/opt/seqtk/seqtk randbase jelly.out.fasta |/opt/seqtk/seqtk seq -U > ../jelly.out.upper.fasta
#########################
# STEP 12 Run a variant caller or use Pilon (twice)
# to correct indels in jelly.out.fasta PacBio filled in Gaps using Illumina reads
#########################
## personally, whether you use Pilon or a Variant Caller (such as callvariants.sh from BBTools), I found that mapping with BBMap with the vslow=t option had better indel correction for simulated data
## for real data, using the steps below outperformed Pilon in terms of better RNA-Seq mapping rates
##
## presumably you can use your 10x reads to correct indels?
## calling this paired-end read file as 10x-illumina-quality-controlled-and-trimmed-reads.fq.gz in steps below
#########################
# STEP 13 Error correct with BBMap once
#########################
cd /genetics/user
# download latest version of BBTools
wget https://sourceforge.net/projects/bbmap/files/BBMap_38.25.tar.gz
tar xzf BBMap_38.25.tar.gz
cd bbmap
# compile jni components
cd jni
# add to ~/.bashrc export JAVA_HOME="/usr/lib/jvm/java-1.8.0-openjdk-amd64" or where ever your jvm machine is installed
# then source ~/.bashrc
make -f makefile.linux
cd ${WorkDir}
# map reads with bbmap 38.25 in vslow mode using jni
/genetics/user/bbmap/bbmap.sh -Xmx350g -eoom usejni=t pigz=t threads=75 vslow=t ref=jelly.out.upper.fasta in=10x-illumina-quality-controlled-and-trimmed-reads.fq.gz \
out=10x-illumina-quality-controlled-and-trimmed-reads-mapped-to-jelly.out.upper.fasta-using-bbmap.bam overwrite=t 2> bbmap.log &
# callvariants 38.25
/genetics/user/bbmap/callvariants.sh -Xmx350g threads=75 ref=jelly.out.upper.fasta in=10x-illumina-quality-controlled-and-trimmed-reads-mapped-to-jelly.out.upper.fasta-using-bbmap.sorted.bam \
ploidy=2 vcf=10x-illumina-quality-controlled-and-trimmed-reads-mapped-to-jelly.out.upper.fasta-using-bbmap.vcf minscore=20.0 overwrite=t 2> callvariants.log &
# use bgzip and tabix to compress then index vcf file
bgzip -f 10x-illumina-quality-controlled-and-trimmed-reads-mapped-to-jelly.out.upper.fasta-using-bbmap.vcf
tabix -p vcf 10x-illumina-quality-controlled-and-trimmed-reads-mapped-to-jelly.out.upper.fasta-using-bbmap.vcf.gz
# use bcftools to get consensus sequence
bcftools consensus -f jelly.out.upper.fasta 10x-illumina-quality-controlled-and-trimmed-reads-mapped-to-jelly.out.upper.fasta-using-bbmap.vcf.gz -o jelly.out.upper.bbmap-1.fasta 2> bcftools.log &
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