/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.fa /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1
/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.fa /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1
/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.fa /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1
/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.fa /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1
/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.fa /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1
/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20