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00_deprecated
00_deprecated
 
 
.gitignore
.gitignore
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
argparse_example.py
argparse_example.py
 
 
avg
avg
 
 
aviti_reorganize_folder.sh
aviti_reorganize_folder.sh
 
 
beagle_extract_wanted_snps.py
beagle_extract_wanted_snps.py
 
 
beagle_remove_unwanted.py
beagle_remove_unwanted.py
 
 
beagle_sliding_window.py
beagle_sliding_window.py
 
 
beagle_split_by_n_samples.py
beagle_split_by_n_samples.py
 
 
body.sh
body.sh
 
 
complexity_by_sliding_windows.py
complexity_by_sliding_windows.py
 
 
compress_directories
compress_directories
 
 
datify.sh
datify.sh
 
 
estimate_numreads_per_sample.sh
estimate_numreads_per_sample.sh
 
 
fasta_GC_disctibution_graph.py
fasta_GC_disctibution_graph.py
 
 
fasta_complexity_by_sequence.py
fasta_complexity_by_sequence.py
 
 
fasta_complexity_by_sliding_windows.py
fasta_complexity_by_sliding_windows.py
 
 
fasta_count_kmers.py
fasta_count_kmers.py
 
 
fasta_deinterleave.sh
fasta_deinterleave.sh
 
 
fasta_digest.py
fasta_digest.py
 
 
fasta_extract.py
fasta_extract.py
 
 
fasta_extract_first_only.py
fasta_extract_first_only.py
 
 
fasta_extract_flanking_regions.py
fasta_extract_flanking_regions.py
 
 
fasta_extract_group.py
fasta_extract_group.py
 
 
fasta_extract_max_length.py
fasta_extract_max_length.py
 
 
fasta_extract_min_coverage.py
fasta_extract_min_coverage.py
 
 
fasta_extract_min_length.py
fasta_extract_min_length.py
 
 
fasta_extract_n_sequences.py
fasta_extract_n_sequences.py
 
 
fasta_extract_name.py
fasta_extract_name.py
 
 
fasta_extract_nucleotides_at_positions.py
fasta_extract_nucleotides_at_positions.py
 
 
fasta_extract_random_sequences.py
fasta_extract_random_sequences.py
 
 
fasta_extract_scaffold_regions.py
fasta_extract_scaffold_regions.py
 
 
fasta_extract_wo_indel.py
fasta_extract_wo_indel.py
 
 
fasta_keep_first.py
fasta_keep_first.py
 
 
fasta_lengths.py
fasta_lengths.py
 
 
fasta_longer_nb.py
fasta_longer_nb.py
 
 
fasta_mask_regions.py
fasta_mask_regions.py
 
 
fasta_max_len.py
fasta_max_len.py
 
 
fasta_mean_len.py
fasta_mean_len.py
 
 
fasta_min_len.py
fasta_min_len.py
 
 
fasta_n50.py
fasta_n50.py
 
 
fasta_n50_one_line.py
fasta_n50_one_line.py
 
 
fasta_nstats.py
fasta_nstats.py
 
 
fasta_number_sequences.py
fasta_number_sequences.py
 
 
fasta_random.py
fasta_random.py
 
 
fasta_random_length.py
fasta_random_length.py
 
 
fasta_remove.py
fasta_remove.py
 
 
fasta_remove_duplicates.py
fasta_remove_duplicates.py
 
 
fasta_remove_regions.py
fasta_remove_regions.py
 
 
fasta_remove_sequences_with_N.py
fasta_remove_sequences_with_N.py
 
 
fasta_remove_start.py
fasta_remove_start.py
 
 
fasta_rename_matepair.py
fasta_rename_matepair.py
 
 
fasta_rename_sequences.py
fasta_rename_sequences.py
 
 
fasta_replace_short_reads.py
fasta_replace_short_reads.py
 
 
fasta_reservoir_sampling.py
fasta_reservoir_sampling.py
 
 
fasta_reverse_comp.py
fasta_reverse_comp.py
 
 
fasta_reverse_comp_specified_sequences.py
fasta_reverse_comp_specified_sequences.py
 
 
fasta_separate_tags.py
fasta_separate_tags.py
 
 
fasta_sort_sequences_by_name.py
fasta_sort_sequences_by_name.py
 
 
fasta_split.py
fasta_split.py
 
 
fasta_split_long_sequences.py
fasta_split_long_sequences.py
 
 
fasta_split_n_nucleotides.py
fasta_split_n_nucleotides.py
 
 
fasta_split_scaffolds.py
fasta_split_scaffolds.py
 
 
fasta_split_sliding_window.py
fasta_split_sliding_window.py
 
 
fasta_to_fake_fastq.py
fasta_to_fake_fastq.py
 
 
fasta_to_simple_agp.py
fasta_to_simple_agp.py
 
 
fasta_total_length.py
fasta_total_length.py
 
 
fasta_total_length.sh
fasta_total_length.sh
 
 
fasta_unwrap.py
fasta_unwrap.py
 
 
fasta_wrap.py
fasta_wrap.py
 
 
fastqCombinePairedEnd.py
fastqCombinePairedEnd.py
 
 
fastq_deinterleave.sh
fastq_deinterleave.sh
 
 
fastq_exclude.py
fastq_exclude.py
 
 
fastq_extract.py
fastq_extract.py
 
 
fastq_min_length.py
fastq_min_length.py
 
 
fastq_min_max_length.py
fastq_min_max_length.py
 
 
fastq_remove.py
fastq_remove.py
 
 
fastq_reservoir_sampling.py
fastq_reservoir_sampling.py
 
 
fastq_split.py
fastq_split.py
 
 
fastq_split_to_4_files.py
fastq_split_to_4_files.py
 
 
fastq_to_fasta.py
fastq_to_fasta.py
 
 
fastq_to_trimmed_fasta.py
fastq_to_trimmed_fasta.py
 
 
fastq_trim.py
fastq_trim.py
 
 
fastqgz_subsampling.py
fastqgz_subsampling.py
 
 
fastqslim.py
fastqslim.py
 
 
gmailsend.py
gmailsend.py
 
 
line_extract.py
line_extract.py
 
 
line_remove.py
line_remove.py
 
 
markers_extract_to_file.py
markers_extract_to_file.py
 
 
markers_extract_to_screen.py
markers_extract_to_screen.py
 
 
merge_alternate_columns.py
merge_alternate_columns.py
 
 
number_add_zeros.py
number_add_zeros.py
 
 
number_pad_spaces.py
number_pad_spaces.py
 
 
parse_dupes.py
parse_dupes.py
 
 
plot
plot
 
 
plot2
plot2
 
 
plot2lines
plot2lines
 
 
plotlines
plotlines
 
 

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About these scripts

This is a collection of scripts written over the years to solve specific problems. Some of them are well tested, others not so well. As they have been written over a period of 13+ years, the style and quality vary considerably.

USE AT YOUR OWN RISK

These programs are provided as is, without any implied garanty of usefulness.

Licensing

Read the LICENSE file for information about the license affecting these files

About

Collection of various scripts

Topics

scripts scripts-collection random-scripts

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Readme

License

GPL-3.0 license
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