├── .gitignore ├── LICENSE ├── README.md ├── R_functions ├── fixed_bin_historgram.R └── getNX.R ├── bam2coverage.sh ├── bam2extract_by_list_of_headers.py ├── bam2fastq_filtered.py ├── bam2fastq_mapped_to_specific_contigs.py ├── bam2fastq_mapped_to_specific_contigs.sh ├── blast_filter.py ├── depth2bed_coverage.py ├── depth2depth_per_contig.awk ├── depth2depth_per_contig.py ├── depth2depth_per_contig_median.py ├── fasta2extract_by_header.py ├── fasta2extract_by_list_of_headers.py ├── fasta2extract_by_nt_range.py ├── fasta2fasta_annotated_portions.py ├── fasta2fasta_length_filtering.py ├── fasta2genomic_stats.py ├── fasta2lengths.py ├── fasta2nameslengths.py ├── fasta2number_of_N.sh ├── fasta2unmasked_fasta.py ├── fastq.gz2number_of_nt.sh ├── fastq2fasta_length_filtering.py ├── fastq2fastq_length_filtering.py ├── gtk2cds.py ├── sync2bed.py └── test ├── data ├── Makefile └── five_scaffolds.fa.gz └── test_bam2fastq_filtered.sh /.gitignore: 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