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00_deprecated
00_deprecated
 
 
.gitignore
.gitignore
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
argparse_example.py
argparse_example.py
 
 
avg
avg
 
 
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_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_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_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_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
 
 
progress_bar.py
progress_bar.py
 
 
reduce_photos.sh
reduce_photos.sh
 
 
reduce_png.sh
reduce_png.sh
 
 
rename_scaffolds.py
rename_scaffolds.py
 
 
rename_scaffolds_shortname.py
rename_scaffolds_shortname.py
 
 

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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

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Collection of various scripts

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scripts scripts-collection random-scripts

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License

GPL-3.0 license
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