Fusarium oxysporum f.sp. pisi (PacBio Sequences)

Commands used for the analysis of F.oxysporum f.sp pisi sequences from PacBio

cp /home/armita/generic_profiles/2016-07-28/.generic_profile ~/.profile

(change the dates for future updates)

To look at your profile:

less ~/.profile

OR cd /home/armita less .profile

You will find your files in:

ls /home/miseq_data/pacbio/2017/John_Clarkson_UWAR.JC.ENQ-1929

and your seqs are:

S1 (FOP1) = Fusarium oxysporum f.sp. pisi S2 (FOP2) = Fusarium oxysporum f.sp. pisi S3R1 (FOP5) = Fusarium oxysporum f.sp. pisi

Building a directory structure

	RawDatDir=/home/miseq_data/pacbio/2017/John_Clarkson_UWAR.JC.ENQ-1929
	ProjectDir=/home/groups/harrisonlab/project_files/fusarium_ex_pea
	mkdir -p $ProjectDir/raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1
	mkdir -p $ProjectDir/raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2
	mkdir -p $ProjectDir/raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5

Sequence data was moved into appropriate directories

	RawDatDir=/home/miseq_data/pacbio/2017/John_Clarkson_UWAR.JC.ENQ-1929
	ProjectDir=/home/groups/harrisonlab/project_files/fusarium_ex_pea
	cp $RawDatDir/John_Clarkson_UWAR.JC.ENQ-1929_S1.tar.gz $ProjectDir/raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1
	cp $RawDatDir/John_Clarkson_UWAR.JC.ENQ-1929_S1_raw_reads.tar.gz $ProjectDir/raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1
	cp $RawDatDir/John_Clarkson_UWAR.JC.ENQ-1929_R_S2.tar.gz $ProjectDir/raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2
	cp $RawDatDir/John_Clarkson_UWAR.JC.ENQ-1929_R_S3R1.tar.gz $ProjectDir/raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5

Data was extracted for each isolate and concatenated

FOP2 extracted

	cd raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2
	tar -zxvf John_Clarkson_UWAR.JC.ENQ-1929_R_S2.tar.gz

FOP5 extracted

	cd raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5
	tar -zxvf John_Clarkson_UWAR.JC.ENQ-1929_R_S3R1.tar.gz

FOP1 (both files) extracted

	cd raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1
	tar -zxvf John_Clarkson_UWAR.JC.ENQ-1929_S1_raw_reads.tar.gz
	tar -zxvf John_Clarkson_UWAR.JC.ENQ-1929_S1.tar.gz

FOP2 concatenated

	OutDir=raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2/extracted
	mkdir -p $OutDir
	for H5_File in $(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2/*/raw_reads/*/Analysis_Results/*.bas.h5); do
	ReadSet=$(echo $H5_File | rev | cut -f3 -d '/' | rev)
	bash5tools.py $H5_File --outFile $OutDir/FOP2_pacbio_$ReadSet --outType fastq --readType unrolled --minLength 100
	done
	cat raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2/*/raw_reads/*/Analysis_Results/*.subreads.fastq > $OutDir/concatenated_pacbio.fastq

FOP5 concatenated

	OutDir=raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5/extracted
	mkdir -p $OutDir
	for H5_File in $(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5/*/raw_reads/*/Analysis_Results/*.bas.h5); do
	ReadSet=$(echo $H5_File | rev | cut -f3 -d '/' | rev)
	bash5tools.py $H5_File --outFile $OutDir/FOP5_pacbio_$ReadSet --outType fastq --readType unrolled --minLength 100
	done
	cat raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5/*/raw_reads/*/Analysis_Results/*.subreads.fastq > $OutDir/concatenated_pacbio.fastq

FOP1 concatenated

	OutDir=raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1/extracted
	mkdir -p $OutDir
	for H5_File in $(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1/*raw_reads/*/Analysis_Results/*.bas.h5); do
	ReadSet=$(echo $H5_File | rev | cut -f3 -d '/' | rev)
	bash5tools.py $H5_File --outFile $OutDir/FOP1_pacbio_$ReadSet --outType fastq --readType unrolled --minLength 100
	done
	cat raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1/*/*/Analysis_Results/*.subreads.fastq > $OutDir/concatenated_pacbio.fastq

had to change the file structure in last line: From: raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1//raw_reads//Analysis_Results/.subreads.fastq To: raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1///Analysis_Results/*.subreads.fastq

**No fastq files or h5 files in John_Clarkson_UWAR.JC.ENQ-1929_S1.tar.gz **

Canu Assembly

FOP2 assembly

	Reads=$(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2/extracted/concatenated_pacbio.fastq)
  	GenomeSz="50m"
  	Strain=$(echo $Reads | rev | cut -f3 -d '/' | rev)
  	Organism=$(echo $Reads | rev | cut -f4 -d '/' | rev)
  	Prefix="$Strain"_canu
  	OutDir="assembly/canu-1.3/$Organism/$Strain"_canu
  	ProgDir=~/git_repos/tools/seq_tools/assemblers/canu
  	qsub $ProgDir/submit_canu.sh $Reads $GenomeSz $Prefix $OutDir

FOP2 assembly

		Reads=$(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2/extracted/concatenated_pacbio.fastq)
  	GenomeSz="55m"
  	Strain=$(echo $Reads | rev | cut -f3 -d '/' | rev)
  	Organism=$(echo $Reads | rev | cut -f4 -d '/' | rev)
  	Prefix="$Strain"_canu
  	OutDir="assembly/canu-1.6/$Organism/$Strain"_canu
  	ProgDir=/home/armita/git_repos/emr_repos/tools/seq_tools/assemblers/canu
  	qsub $ProgDir/submit_canu.sh $Reads $GenomeSz $Prefix $OutDir

FOP5 assembly

	Reads=$(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5/extracted/concatenated_pacbio.fastq)
 	GenomeSz="50m"
  	Strain=$(echo $Reads | rev | cut -f3 -d '/' | rev)
  	Organism=$(echo $Reads | rev | cut -f4 -d '/' | rev)
  	Prefix="$Strain"_canu
  	OutDir="assembly/canu-1.3/$Organism/$Strain"_canu
  	ProgDir=~/git_repos/tools/seq_tools/assemblers/canu
  	qsub $ProgDir/submit_canu.sh $Reads $GenomeSz $Prefix $OutDir

FOP1 assembly

	Reads=$(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1/extracted/concatenated_pacbio.fastq)
	GenomeSz="50m"
	Strain=$(echo $Reads | rev | cut -f3 -d '/' | rev)
	Organism=$(echo $Reads | rev | cut -f4 -d '/' | rev)
	Prefix="$Strain"_canu
	OutDir="assembly/canu-1.3/$Organism/$Strain"_canu
	ProgDir=~/git_repos/tools/seq_tools/assemblers/canu
	qsub $ProgDir/submit_canu.sh $Reads $GenomeSz $Prefix $OutDir

Assembly stats were collected using quast

FOP2

	ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		for Assembly in $(ls assembly/canu-1.3/*/FOP2_canu/*_canu.contigs.fasta); do
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		OutDir=assembly/canu-1.3/$Organism/$Strain/filtered_contigs
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done

FOP5

	ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		for Assembly in $(ls assembly/canu-1.3/*/FOP5_canu/*_canu.contigs.fasta); do
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		OutDir=assembly/canu-1.3/$Organism/$Strain/filtered_contigs
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done

FOP1

	ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		for Assembly in $(ls assembly/canu-1.3/*/FOP1_canu/*_canu.contigs.fasta); do
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		OutDir=assembly/canu-1.3/$Organism/$Strain/filtered_contigs
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done

LOOK AT ASSEMBLY STATS!

Assemblies were polished using Pilon

FOP2

	for Assembly in $(ls assembly/canu-1.3/*/FOP2_canu/FOP2_canu.contigs.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/FOP2)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP2_S1_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP2_S1_L001_R2_001_trim.fq.gz);
		OutDir=assembly/canu/$Organism/$Strain/polished
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/pilon
		qsub $ProgDir/sub_pilon.sh $Assembly $TrimF1_Read $TrimR1_Read $OutDir
	done

FOP5

	for Assembly in $(ls assembly/canu-1.3/*/FOP5_canu/FOP5_canu.contigs.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/FOP5)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP5_S2_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP5_S2_L001_R2_001_trim.fq.gz);
		OutDir=assembly/canu/$Organism/$Strain/polished
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/pilon
		qsub $ProgDir/sub_pilon.sh $Assembly $TrimF1_Read $TrimR1_Read $OutDir
	done

FOP1

	for Assembly in $(ls assembly/canu-1.3/*/FOP1_canu/FOP1_canu.contigs.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/FOP1)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP1_S1_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP1_S1_L001_R2_001_trim.fq.gz);
		OutDir=assembly/canu/$Organism/$Strain/polished
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/pilon
		qsub $ProgDir/sub_pilon.sh $Assembly $TrimF1_Read $TrimR1_Read $OutDir
	done

Spades Assembly

FOP2

	for PacBioDat in $(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP2/extracted/concatenated_pacbio.fastq); do
		Organism=$(echo $PacBioDat | rev | cut -f4 -d '/' | rev)
		Strain=$(echo $PacBioDat | rev | cut -f3 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/$Strain)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP2_S1_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP2_S1_L001_R2_001_trim.fq.gz);
		OutDir=assembly/spades_pacbio/$Organism/"$Strain"
		echo $TrimR1_Read
		echo $TrimR1_Read
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/spades
		qsub $ProgDir/sub_spades_pacbio.sh $PacBioDat $TrimF1_Read $TrimR1_Read $OutDir 20
	done

FOP5

	for PacBioDat in $(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP5/extracted/concatenated_pacbio.fastq); do
		Organism=$(echo $PacBioDat | rev | cut -f4 -d '/' | rev)
		Strain=$(echo $PacBioDat | rev | cut -f3 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/$Strain)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP5_S2_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP5_S2_L001_R2_001_trim.fq.gz);
		OutDir=assembly/spades_pacbio/$Organism/"$Strain"
		echo $TrimR1_Read
		echo $TrimR1_Read
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/spades
		qsub $ProgDir/sub_spades_pacbio.sh $PacBioDat $TrimF1_Read $TrimR1_Read $OutDir 20
	done

FOP1

	for PacBioDat in $(ls raw_dna/pacbio/F.oxysporum_fsp_pisi/FOP1/extracted/concatenated_pacbio.fastq); do
		Organism=$(echo $PacBioDat | rev | cut -f4 -d '/' | rev)
		Strain=$(echo $PacBioDat | rev | cut -f3 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/$Strain)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP1_S1_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP1_S1_L001_R2_001_trim.fq.gz);
		OutDir=assembly/spades_pacbio/$Organism/"$Strain"
		echo $TrimR1_Read
		echo $TrimR1_Read
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/spades
		qsub $ProgDir/sub_spades_pacbio.sh $PacBioDat $TrimF1_Read $TrimR1_Read $OutDir 20
	done

ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
for Assembly in $(ls assembly/spades_pacbio/*/FOP1/contigs.fasta); do
Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
OutDir=assembly/spades_pacbio/$Organism/$Strain/quast
qsub $ProgDir/sub_quast.sh $Assembly $OutDir
done

#Contigs shorter than 500bp were removed from the assembly

FOP1

	for Contigs in $(ls assembly/spades_pacbio/*/FOP1/contigs.fasta); do
		AssemblyDir=$(dirname $Contigs)
		mkdir $AssemblyDir/filtered_contigs
		FilterDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/abyss
		$FilterDir/filter_abyss_contigs.py $Contigs 500 > $AssemblyDir/filtered_contigs/contigs_min_500bp.fasta
	done

FOP2

	for Contigs in $(ls assembly/spades_pacbio/*/FOP2/contigs.fasta); do
		AssemblyDir=$(dirname $Contigs)
		mkdir $AssemblyDir/filtered_contigs
		FilterDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/abyss
		$FilterDir/filter_abyss_contigs.py $Contigs 500 > $AssemblyDir/filtered_contigs/contigs_min_500bp.fasta
	done

FOP5

	for Contigs in $(ls assembly/spades_pacbio/*/FOP5/contigs.fasta); do
		AssemblyDir=$(dirname $Contigs)
		mkdir $AssemblyDir/filtered_contigs
		FilterDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/abyss
		$FilterDir/filter_abyss_contigs.py $Contigs 500 > $AssemblyDir/filtered_contigs/contigs_min_500bp.fasta
	done

Merging pacbio and hybrid assemblies

FOP1

Can run the quickmerge prog with $PacBioAssembly first or $HybridAssembly first. Try both and then do quast for both and see which has the lowest number of contigs and check the genome size

Merging 1

	for PacBioAssembly in $(ls assembly/canu/F.oxysporum_fsp_pisi/FOP1_canu/polished/pilon.fasta); do
		Organism=$(echo $PacBioAssembly | rev | cut -f4 -d '/' | rev)
		Strain=FOP1
		HybridAssembly=$(ls assembly/spades_pacbio/$Organism/$Strain/contigs.fasta)
		OutDir=assembly/merged_canu_spades/$Organism/$Strain
		AnchorLength=100000
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/quickmerge
<<<<<<< HEAD
		qsub $ProgDir/sub_quickmerge.sh $PacBioAssembly $HybridAssembly $OutDir $AnchorLength
	done

Merging 2

	for PacBioAssembly in $(ls assembly/canu/F.oxysporum_fsp_pisi/FOP1_canu/polished/pilon.fasta); do
		Organism=$(echo $PacBioAssembly | rev | cut -f4 -d '/' | rev)
		Strain=FOP1
		HybridAssembly=$(ls assembly/spades_pacbio/$Organism/$Strain/contigs.fasta)
		OutDir=assembly/merged_canu_spades/$Organism/"$Strain"_reversed_order
		AnchorLength=100000
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/quickmerge
		qsub $ProgDir/sub_quickmerge.sh $HybridAssembly $PacBioAssembly $OutDir $AnchorLength
	done

quast for each variation of merging

Merge1

	ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		for Assembly in $(ls assembly/merged_canu_spades/F.oxysporum_fsp_pisi/FOP1/merged.fasta); do
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		OutDir=assembly/merged_canu_spades/$Organism/$Strain/quast_merged1
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done

Merge2

	ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		for Assembly in $(ls assembly/merged_canu_spades/F.oxysporum_fsp_pisi/FOP1_reversed_order/merged.fasta); do
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		OutDir=assembly/merged_canu_spades/$Organism/FOP1_reversed_order/quast_merged2
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
=======
		qsub $ProgDir/sub_quickmerge.sh $PacBioAssembly $HybridAssembly $OutDir

	done

COMPARE THESE quasts and choose for below scripts... if its the first one you've already done it.

Remove contaminants and renames files

	touch tmp.csv
		for Assembly in $(ls assembly/merged_canu_spades/F.oxysporum_fsp_pisi/FOP1/merged.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		OutDir=$(dirname $Assembly)
		mkdir -p $OutDir
		ProgDir=~/git_repos/tools/seq_tools/assemblers/assembly_qc/remove_contaminants
		$ProgDir/remove_contaminants.py --inp $Assembly --out $OutDir/"$Strain"_contigs_renamed.fasta --coord_file tmp.csv
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done
	rm tmp.csv

output of ^ assembly/merged_canu_spades/F.oxysporum_fsp_pisi/FOP1/FOP1_contigs_renamed.fasta

Merged assembly polished using Pilon

	for Assembly in $(ls assembly/merged_canu_spades/*/FOP1/FOP1_contigs_renamed.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/$Strain)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP1_S1_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP1_S1_L001_R2_001_trim.fq.gz);
		OutDir=assembly/merged_canu_spades/$Organism/$Strain/polished
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/pilon
		qsub $ProgDir/sub_pilon.sh $Assembly $TrimF1_Read $TrimR1_Read $OutDir
	done

DO THIS? Remove contaminants and rename

ProgDir=~/git_repos/tools/seq_tools/assemblers/assembly_qc/remove_contaminants
  touch tmp.csv
  # for Assembly in $(ls assembly/merged_canu_spades/*/*/polished/pilon.fasta); do
  # for Assembly in $(ls assembly/pacbio_test/F.oxysporum_fsp_cepae/Fus2_pacbio_merged/polished/pilon.fasta); do
    for Assembly in $(ls assembly/merged_canu_spades/F.oxysporum_fsp_cepae/Fus2_edited2/polished/pilon.fasta); do
  # for Assembly in $(ls assembly/merged_canu_spades/F.oxysporum_fsp_cepae/Fus2_edited2/polished/pilon.fasta); do
    Organism=$(echo $Assembly | rev | cut -f4 -d '/' | rev)  
    Strain=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
    # OutDir=assembly/merged_canu_spades/$Organism/$Strain/filtered_contigs
    OutDir=assembly/merged_canu_spades/$Organism/$Strain/filtered_contigs
    mkdir -p $OutDir
    $ProgDir/remove_contaminants.py --inp $Assembly --out $OutDir/"$Strain"_contigs_renamed.fasta --coord_file tmp.csv
  done
  rm tmp.csv

FOP2

Merging

	for PacBioAssembly in $(ls assembly/canu/F.oxysporum_fsp_pisi/FOP2_canu/polished/pilon.fasta); do
		Organism=$(echo $PacBioAssembly | rev | cut -f4 -d '/' | rev)
		Strain=FOP2
		HybridAssembly=$(ls assembly/spades_pacbio/$Organism/$Strain/contigs.fasta)
		OutDir=assembly/merged_canu_spades/$Organism/$Strain
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/quickmerge
		qsub $ProgDir/sub_quickmerge.sh $PacBioAssembly $HybridAssembly $OutDir
	done

Remove contaminants and rename

	touch tmp.csv
		for Assembly in $(ls assembly/merged_canu_spades/F.oxysporum_fsp_pisi/FOP2/merged.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		OutDir=$(dirname $Assembly)
		mkdir -p $OutDir
		ProgDir=~/git_repos/tools/seq_tools/assemblers/assembly_qc/remove_contaminants
		$ProgDir/remove_contaminants.py --inp $Assembly --out $OutDir/"$Strain"_contigs_renamed.fasta --coord_file tmp.csv
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done
	rm tmp.csv

Merged assembly polished using Pilon

	for Assembly in $(ls assembly/merged_canu_spades/*/FOP2/FOP2_contigs_renamed.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/$Strain)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP2_S1_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP2_S1_L001_R2_001_trim.fq.gz);
		OutDir=assembly/merged_canu_spades/$Organism/$Strain/polished
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/pilon
		qsub $ProgDir/sub_pilon.sh $Assembly $TrimF1_Read $TrimR1_Read $OutDir
	done

FOP5

Merging

	for PacBioAssembly in $(ls assembly/canu/F.oxysporum_fsp_pisi/FOP5_canu/polished/pilon.fasta); do
		Organism=$(echo $PacBioAssembly | rev | cut -f4 -d '/' | rev)
		Strain=FOP5
		HybridAssembly=$(ls assembly/spades_pacbio/$Organism/$Strain/contigs.fasta)
		OutDir=assembly/merged_canu_spades/$Organism/$Strain
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/quickmerge
		qsub $ProgDir/sub_quickmerge.sh $PacBioAssembly $HybridAssembly $OutDir
	done

Remove contaminants and rename

	touch tmp.csv
		for Assembly in $(ls assembly/merged_canu_spades/F.oxysporum_fsp_pisi/FOP5/merged.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)  
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		OutDir=$(dirname $Assembly)
		mkdir -p $OutDir
		ProgDir=~/git_repos/tools/seq_tools/assemblers/assembly_qc/remove_contaminants
		$ProgDir/remove_contaminants.py --inp $Assembly --out $OutDir/"$Strain"_contigs_renamed.fasta --coord_file tmp.csv
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done
	rm tmp.csv

Merged assembly polished using Pilon

	for Assembly in $(ls assembly/merged_canu_spades/*/FOP5/FOP5_contigs_renamed.fasta); do
		Organism=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
		Strain=$(echo $Assembly | rev | cut -f2 -d '/' | rev)
		IlluminaDir=$(ls -d qc_dna/paired/$Organism/$Strain)
		TrimF1_Read=$(ls $IlluminaDir/F/FOP5_S2_L001_R1_001_trim.fq.gz);
		TrimR1_Read=$(ls $IlluminaDir/R/FOP5_S2_L001_R2_001_trim.fq.gz);
		OutDir=assembly/merged_canu_spades/$Organism/$Strain/polished
		ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/pilon
		qsub $ProgDir/sub_pilon.sh $Assembly $TrimF1_Read $TrimR1_Read $OutDir
	done

Assembly stats were collected using Quast REPEAT

	ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
		for Assembly in $(ls assembly/merged_canu_spades/*/*/polished/pilon.fasta); do
		Strain=$(echo $Assembly | rev | cut -f3 -d '/' | rev)
		Organism=$(echo $Assembly | rev | cut -f4 -d '/' | rev)  
		OutDir=assembly/merged_canu_spades/$Organism/$Strain/polished
		qsub $ProgDir/sub_quast.sh $Assembly $OutDir
	done

Repeat masking REPEAT

Repeat masking of canu assemblies (polished)

	ProgDir=/home/jenkis/git_repos/tools/seq_tools/repeat_masking
		for Assembly in $(ls assembly/canu/*/*/polished/pilon.fasta); do
		qsub $ProgDir/rep_modeling.sh $Assembly
		qsub $ProgDir/transposonPSI.sh $Assembly
	done

merging assemblies

```bash
for PacBioAssembly in $(ls assembly/canu/F.oxysporum_fsp_pisi/FOP1_canu/polished/pilon.fasta); do
	Organism=$(echo $PacBioAssembly | rev | cut -f4 -d '/' | rev)
	Strain=FOP1
	HybridAssembly=$(ls assembly/spades_pacbio/$Organism/"$Strain"_etc/contigs.fasta)
	OutDir=assembly/merged_canu_spades/$Organism/$Strain
	ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/quickmerge
	qsub $ProgDir/sub_quickmerge.sh $PacBioAssembly $HybridAssembly $OutDir     *change order of PacBioAssemly and HybridAssembly
done

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Pacbio.md

Pacbio.md

Fusarium oxysporum f.sp. pisi (PacBio Sequences)

Commands used for the analysis of F.oxysporum f.sp pisi sequences from PacBio

Building a directory structure

Sequence data was moved into appropriate directories

Data was extracted for each isolate and concatenated

Canu Assembly

Assembly stats were collected using quast

Assemblies were polished using Pilon

Spades Assembly

Merging pacbio and hybrid assemblies

Assembly stats were collected using Quast REPEAT

Repeat masking REPEAT

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Pacbio.md

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Pacbio.md

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Fusarium oxysporum f.sp. pisi (PacBio Sequences)

Commands used for the analysis of F.oxysporum f.sp pisi sequences from PacBio

Building a directory structure

Sequence data was moved into appropriate directories

Data was extracted for each isolate and concatenated

Canu Assembly

Assembly stats were collected using quast

Assemblies were polished using Pilon

Spades Assembly

Merging pacbio and hybrid assemblies

Assembly stats were collected using Quast REPEAT

Repeat masking REPEAT