bioinfo-scripts

My personal collection of (mostly) bioinformatics-related scripts.

Scripts are usually and written in Perl, Bash, and whatever was just available.

Work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Name		Name	Last commit message	Last commit date
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
biodb_genome_downloader.sh		biodb_genome_downloader.sh
biomart_retrieve_rRNA.pl		biomart_retrieve_rRNA.pl
circtools_create_detect_files_paired.sh		circtools_create_detect_files_paired.sh
circtools_create_detect_files_paired_CD.sh		circtools_create_detect_files_paired_CD.sh
circtools_create_detect_files_single.sh		circtools_create_detect_files_single.sh
circtools_merge_enrich_results.sh		circtools_merge_enrich_results.sh
create_user.py		create_user.py
random_downsample_bam.sh		random_downsample_bam.sh
rename_raw_file.pl		rename_raw_file.pl
slurm_7z_gz_test.sh		slurm_7z_gz_test.sh
slurm_albacore.sh		slurm_albacore.sh
slurm_ballgown.sh		slurm_ballgown.sh
slurm_bam_to_bw.sh		slurm_bam_to_bw.sh
slurm_bamtools.sh		slurm_bamtools.sh
slurm_blastn.sh		slurm_blastn.sh
slurm_bonito_train.sh		slurm_bonito_train.sh
slurm_bowtie2_find_circ_paired.sh		slurm_bowtie2_find_circ_paired.sh
slurm_bowtie2_rRNA_filter_circtools_book_2023.sh		slurm_bowtie2_rRNA_filter_circtools_book_2023.sh
slurm_bowtie2_rRNA_filter_paired.sh		slurm_bowtie2_rRNA_filter_paired.sh
slurm_bowtie2_rRNA_filter_paired_make.sh		slurm_bowtie2_rRNA_filter_paired_make.sh
slurm_bowtie2_rRNA_filter_single.sh		slurm_bowtie2_rRNA_filter_single.sh
slurm_bowtie2_rRNA_filter_single_make.sh		slurm_bowtie2_rRNA_filter_single_make.sh
slurm_bowtie2_selector_paired.sh		slurm_bowtie2_selector_paired.sh
slurm_circtools_detect_book_2023.sh		slurm_circtools_detect_book_2023.sh
slurm_circtools_detect_paired.sh		slurm_circtools_detect_paired.sh
slurm_circtools_detect_paired_mapping.sh		slurm_circtools_detect_paired_mapping.sh
slurm_circtools_detect_paired_mapping_make.sh		slurm_circtools_detect_paired_mapping_make.sh
slurm_circtools_detect_paired_mapping_old.sh		slurm_circtools_detect_paired_mapping_old.sh
slurm_circtools_detect_paired_postprocess.sh		slurm_circtools_detect_paired_postprocess.sh
slurm_circtools_detect_single.sh		slurm_circtools_detect_single.sh
slurm_circtools_detect_single_mapping_make.sh		slurm_circtools_detect_single_mapping_make.sh
slurm_circtools_detect_unpaired.sh		slurm_circtools_detect_unpaired.sh
slurm_circtools_detect_unpaired_mapping.sh		slurm_circtools_detect_unpaired_mapping.sh
slurm_circtools_enrich_exon.sh		slurm_circtools_enrich_exon.sh
slurm_circtools_enrich_gene.sh		slurm_circtools_enrich_gene.sh
slurm_circtools_enrich_intron.sh		slurm_circtools_enrich_intron.sh
slurm_circtools_prepare_book_2023.sh		slurm_circtools_prepare_book_2023.sh
slurm_circtools_reconstruct.sh		slurm_circtools_reconstruct.sh
slurm_circtools_reconstruct_3.sh		slurm_circtools_reconstruct_3.sh
slurm_circtools_reconstruct_CD.sh		slurm_circtools_reconstruct_CD.sh
slurm_circtools_reconstruct_DL.sh		slurm_circtools_reconstruct_DL.sh
slurm_circtools_reconstruct_book_2023.sh		slurm_circtools_reconstruct_book_2023.sh
slurm_circtools_reconstruct_denovo.sh		slurm_circtools_reconstruct_denovo.sh
slurm_create_taiyaki_training_set.sh		slurm_create_taiyaki_training_set.sh
slurm_dcc3.sh		slurm_dcc3.sh
slurm_dexseq.sh		slurm_dexseq.sh
slurm_fast5.sh		slurm_fast5.sh
slurm_fast5_multi.sh		slurm_fast5_multi.sh
slurm_fastqc.sh		slurm_fastqc.sh
slurm_featurecount_paired.sh		slurm_featurecount_paired.sh
slurm_flexbar_paired.sh		slurm_flexbar_paired.sh
slurm_flexbar_paired_100.sh		slurm_flexbar_paired_100.sh
slurm_flexbar_paired_150.sh		slurm_flexbar_paired_150.sh
slurm_flexbar_paired_circtools_book_2023.sh		slurm_flexbar_paired_circtools_book_2023.sh
slurm_flexbar_paired_make.sh		slurm_flexbar_paired_make.sh
slurm_flexbar_single.sh		slurm_flexbar_single.sh
slurm_flexbar_single_make.sh		slurm_flexbar_single_make.sh
slurm_fuchs_denovo.sh		slurm_fuchs_denovo.sh
slurm_fuchs_workflow_paired.sh		slurm_fuchs_workflow_paired.sh
slurm_gpu_template.sh		slurm_gpu_template.sh
slurm_guppy.sh		slurm_guppy.sh
slurm_guppy_new.sh		slurm_guppy_new.sh
slurm_guppy_pascal.sh		slurm_guppy_pascal.sh
slurm_guppy_taiyaki.sh		slurm_guppy_taiyaki.sh
slurm_guppy_taiyaki_cpu.sh		slurm_guppy_taiyaki_cpu.sh
slurm_guppy_taiyaki_p4.sh		slurm_guppy_taiyaki_p4.sh
slurm_guppy_taiyaki_pascal.sh		slurm_guppy_taiyaki_pascal.sh
slurm_guppy_taiyaki_qscore.sh		slurm_guppy_taiyaki_qscore.sh
slurm_guppy_taiyaki_tmp.sh		slurm_guppy_taiyaki_tmp.sh
slurm_guppy_taiyaki_turing.sh		slurm_guppy_taiyaki_turing.sh
slurm_hisat2.sh		slurm_hisat2.sh
slurm_htseq.sh		slurm_htseq.sh
slurm_jacusa.sh		slurm_jacusa.sh
slurm_jacusa2.sh		slurm_jacusa2.sh
slurm_jacusa_call1.sh		slurm_jacusa_call1.sh
slurm_macs2.sh		slurm_macs2.sh
slurm_markcuplicated_picard.sh		slurm_markcuplicated_picard.sh
slurm_minimap2_ont.sh		slurm_minimap2_ont.sh
slurm_minimap2_splice.sh		slurm_minimap2_splice.sh
slurm_multiqc_make.sh		slurm_multiqc_make.sh
slurm_nanocompore_devel.sh		slurm_nanocompore_devel.sh
slurm_nanocompore_main.sh		slurm_nanocompore_main.sh
slurm_nanocompore_preprocess.sh		slurm_nanocompore_preprocess.sh
slurm_nanocompore_preprocess_wo_minimap.sh		slurm_nanocompore_preprocess_wo_minimap.sh
slurm_nanopore_barcoded_reads_per_cell.sh		slurm_nanopore_barcoded_reads_per_cell.sh
slurm_nanopore_step2.sh		slurm_nanopore_step2.sh
slurm_nanopore_step2_single.sh		slurm_nanopore_step2_single.sh
slurm_nanopore_step3.sh		slurm_nanopore_step3.sh
slurm_nanopore_step4.sh		slurm_nanopore_step4.sh
slurm_pbzip2.sh		slurm_pbzip2.sh
slurm_pigz.sh		slurm_pigz.sh
slurm_prepare_subread.sh		slurm_prepare_subread.sh
slurm_rar.sh		slurm_rar.sh
slurm_red.sh		slurm_red.sh
slurm_rpl.sh		slurm_rpl.sh
slurm_salmon.sh		slurm_salmon.sh
slurm_samtools_merge.sh		slurm_samtools_merge.sh

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