cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.biaurelia-Sample_379.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.biaurelia-Sample_76-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.biaurelia-Sample_76-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.biaurelia-Sample_76.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.biaurelia-Sample_USBL-36I1.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.caudatum-Sample_C065.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.caudatum-Sample_C083.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.caudatum-Sample_C104.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.caudatum-Sample_C119-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.caudatum-Sample_C119-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.caudatum-Sample_C119.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.caudatum-Sample_C147-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.caudatum-Sample_C147-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.caudatum-Sample_C147.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.multimicronucleatum-Sample_M03-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.multimicronucleatum-Sample_M03-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.multimicronucleatum-Sample_M03.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.multimicronucleatum-Sample_M04.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.multimicronucleatum-Sample_M05.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.octaurelia-Sample_1038.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_126.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_127.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_128.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_130.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_131.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_132.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_133.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_134.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_137.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_Indo1-7I.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.sexaurelia-Sample_Moz13BIII.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.tetraurelia-Sample_291.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.tetraurelia-Sample_298-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.tetraurelia-Sample_298-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.tetraurelia-Sample_298.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.tetraurelia-Sample_99.50mers.references+mito.unique
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/remapping; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie genome+P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed.mito -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT genome+P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed.mito.fa - | samtools sort - P.tetraurelia-Sample_A.50mers.references+mito.unique