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20150313_LSU_Oil_Spill_IndexID_Comparisons.ipynb
20150316_LSU_OilSpill_Adapter_ID.ipynb
20150317_LSU_OilSpill_EpinextAdaptor1_ID.ipynb
20150408_Install_Bismark_bisulfite_mapper.ipynb
20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb
20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb
20150429_Gigas_larvae_OA_BLASTn.ipynb
20150501_Cgigas_larvae_OA_BLASTn_nt.ipynb
20150506_Cgigas_larvae_OA_trimmomatic_FASTQC.ipynb
20150521_Cgigas_larvae_OA_Trimmomatic_FASTQC.ipynb
20160114_wasted_space_synologies.ipynb
20160126_Olurida_BGI_data_handling.ipynb
20160126_Pgenerosa_BGI_data_handling.ipynb
20160203_Olurida_Zymo_Data_Handling.ipynb
20160308_find_rename_2bRAD_undetermined_fastqs.ipynb
20160314_Olurida_GBS_data_management.ipynb
20160406_Oly_GBS_STACKS.ipynb
20160406_STACKS_install.ipynb
20160411_Concatenate_Oly_MBDseq.ipynb
20160418_Oly_GBS_PE-Pyrad_populations.ipynb
20160418_pyrad_oly_PE-GBS.ipynb
20160427_Oly_GBS_data_management.ipynb
20160427_speed_comparison.ipynb
20160428_Oly_GBS_STACKS.ipynb
20160502_Oly_GBS_barcode_repair.ipynb
20160516_Oly_Small_Insert_Library_Genome_Read_Counts.ipynb
20160523_Oly_GBS_Stacks.ipynb
20160525_pyrad_oly_gbs_bgi.ipynb
20160609_pyrad_oly_gbs_bgi.ipynb
20160714_EC2_Oly_GBS_stacks_analysis.ipynb
20160715_ec2_oly_gbs_pyrad.ipynb
20160816_oly_gbs_fst_calcs.ipynb
20161025_Pgenerosa_Small_Library_Genome_Read_Counts.ipynb
20161117_docker_oly_genome_fastq_corruption.ipynb
20161117_docker_oly_vcf_analysis.ipynb
20161129_docker_R_magics_failure.ipynb
20161206_docker_BGI_genome_downloads.ipynb
20161214_docker_BGI_data_integrity_check.ipynb
20161214_docker_notebook_trimming.ipynb
20161229_docker_genewiz_geoduck_RRBS_data.ipynb
20161230_docker_geoduck_RRBS_md5_checks.ipynb
20170104_docker_oly_BGI_genome_corruption_solved.ipynb
20170227_docker_jay_ngs_data_retrieval.ipynb
20170301_docker_fastqc_nondemultiplexed_bgi_oly_gbs.ipynb
20170306_docker_fastqc_demultiplexed_bgi_oly_gbs.ipynb
20170314_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb
20170320_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb
20170622_oly_pacbio_data_management.ipynb
20170907_docker_pacbio_oly_minimap2.ipynb
20170918_docker_pacbio_oly_miniasm0.2.ipynb
20170918_docker_pacbio_oly_racon0.5.0.ipynb
20171003_docker_oly_assembly_comparisons.ipynb
20171004_docker_oly_redundans.ipynb
20171005_docker_oly_redundans.ipynb
20171018_docker_oly_canu.ipynb
20171023_docker_oly_pacbio_canu_comparisons.ipynb
20171023_docker_oly_redundans.ipynb
20171023_restore_scaphapoda_data.ipynb
20171113_emu_pbjelly_22mer_plat.ipynb
20171114_emu_pbjelly_BGI_scaffold.ipynb
20171114_swoose_oly_assembly_comparisons_quast.ipynb
20171130_emu_pbjelly.ipynb
20180103_emu_pbjelly.ipynb
20180116_swoose_oly_assembly_comparisons_quast.ipynb
20180125_roadrunner_trimming_geoduck_novaseq.ipynb
20180205_roadrunner_meraculous_geoduck_novaseq.ipynb
20180503_emu_oly_methylation_mapping.ipynb
20180508_roadrunner_geoduck_bowtie2_genome_mapping.ipynb
20180514_roadrunner_geoduck_RRBS_trimming.ipynb
20180516_roadrunner_geoduck_EPI_fastqc.ipynb
20180516_roadrunner_geoduck_RRBS_trimming.ipynb
20180523_roadrunner_oly_TEs_repeatmasker.ipynb
20180529_roadrunner_virginica_TEs_repeatmasker.ipynb
20180530_emu_oly_methylation_mapping_deduplication.ipynb
20180702_roadrunner_oly_TEs_repeatmasker.ipynb
20180709_emu_oly_methylation_mapping.ipynb
20180822_roadrunner_virginica_TEs_repeatmasker.ipynb
20180910_roadrunner_virginica_fastqc.ipynb
20180911_roadrunner_virginica_trimgalore.ipynb
20181022_emu_oly_repeatmodeler.ipynb
20181128_swoose_geoduck_vitellogenin_analysis.ipynb
20181211_emu_geo_metagenomics_fastqc_trimgalore.ipynb
20181211_swoose_gigas_mt_primer_design.ipynb
20181212_emu_geo_metagenomics_fastqc_trimgalore.ipynb
20181219_emu_geoduck_repeatmodeler.ipynb
20190103_swoose_C.virginica_vcf_splitting.ipynb
20190110_swoose_geo_metagnomics_metaquast.ipynb
20190225_swoose_CpG_OE.ipynb
20190321_swoose_metagnomics_pgen_blastp_ncbi-sp-v5-db.ipynb
20190327_roadrunner_cgig_TEs_repeatmasker.ipynb
20190418_cvir_mbd_coverage_comparison.ipynb
20190424_swoose_uniprot_go_goslim.ipynb
20190523_pgen_Pgenerosa_v070_gffs.ipynb
20190612_swoose_metagenomics_ind_coverage_krona.ipynb
20190625_swoose_pgen_v070_scaffolds.ipynb
20190626_emu_Pgenerosa_v074_repeatmodeler.ipynb
20190626_roadrunner_Pgeneros_v074_TEs_repeatmasker.ipynb
20190722_swoose_pgen_v070_top18_scaffold_annotation_count.ipynb
20190805_swoose_Pgenerosa_v070_TEs_repeatmasker.ipynb
20190806_roadrunner_Pgenerosa_v070_TEs_repeatmasker.ipynb
20190826_swoose_pgen_genome_feature_counts.ipynb
20190904_swoose_pgen_v074.a3_genome_feature_counts.ipynb
20190905_swoose_pgen_v074.a3_genome_repeats_counts.ipynb
20191022_swoose_pgen_v074.a4_BLAST-GO-mapping.ipynb
20191024_swoose_cbai_fastq_concatenation.ipynb
20191029_swoose_pgen_v074.a4_genome_feature_counts.ipynb
20191029_swoose_pgen_v074.a4_genome_repeats_counts.ipynb
20191030_swoose_pgen_v074.a4_intron_intergenic_features.ipynb
20191031_swoose_pgen_v074_stringtie_BAM_splitting.ipynb
20191105_swoose_pgen_v074_renaming.ipynb
20191106_swoose_pgen_feature_stats.ipynb
20191120_swoose_pgen_v074_renaming.ipynb
20191203_swoose_pgen_v074.a4_genome_feature_counts.ipynb
20191214_olur_genome_feature_and_intron_splitting.ipynb
20200122_swoose_cbai_megan_read_extractions.ipynb
20200131_swoose_cbai_megan_day-treatment_read_extractions.ipynb
20200228_swoose_olur_v081_fasta_renaming.ipynb
20200311_swoose_pgen_genome_ena_submission.ipynb
20200330_swoose_cbai_megan_read_extractions.ipynb
20200413_swoose_cbai_megan_day-treatment_read_extractions.ipynb
20200419_swoose_cbai_megan_day-treatment-temp_read_extractions.ipynb
20200518_swoose_cbai_megan_read_extractions.ipynb
20200730_swoose_geoduck_repro_check.ipynb
20201013_mephisto_cbai_seqtk_megan-fastq-read-extractions.ipynb
20210226_pgen_methylation_gene_IDs.ipynb
20210513_olur_NCBI_genome-submission-prep.ipynb
20210601_ssal_gff-annotations.ipynb
20211209_cvir_gff-to-bed.ipynb
20220217-cvir-lncRNA_subsetting.ipynb
20220301-pgen-gff_to_gtf.ipynb
20220324-pgen-gffs_to_fastas.ipynb
20220419-pgen-gene_annotation_mapping.ipynb
20220818-snam-gff_to_bed-genes.ipynb
20220926_cvir_gff-to-bed-genes_and_pseudogenes.ipynb
20230126-pacu-gff_to_gtf.ipynb
20230127-mcap-gff_to_gtf.ipynb
20230127-pver-gff_to_gtf.ipynb
20230215-pver-GCA_014529365.1-karyotype.ipynb
20230217-cgor-gff_to_gtf.ipynb
20230322-pgen-gene_annotation_update.ipynb
20230502-pgen-lncRNA-identification.ipynb
20230504-pgen-lncRNA-expression.ipynb
20230524-E5-coral-sRNAseq_trimmings_comparisons.ipynb
20230705-pmea-gff_to_gtf.ipynb
20230726-cvir-genes_bed-to-fasta.ipynb
20230730-mmag-megan-fasta_to_fastq.ipynb
InstallingBLAST.ipynb
PE-GBS_empirical.ipynb
PhageNGS.ipynb
PhageNGS_ID.ipynb
template_linux.ipynb
README.md