cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_C026-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_C026-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - Sample_C026-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_M13-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_M13-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - Sample_M13-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Peniche3I-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Peniche3I-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - Sample_Peniche3I-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end2.paired.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie  /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_TRB101-4-SPAdes-3.5.0-trimmed/scaffolds -p 16 -v 3 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_TRB101-4-SPAdes-3.5.0-trimmed/scaffolds.fasta - | samtools sort - Sample_TRB101-4-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique