LIST OF PROGRAMS

* blastn.py: Runs BLAST over the Internet for all the FAS files of the working directory.
* concatenateFastaFiles.py: Concatenates *.fasta files in the working directory
* countReads.py: Counts the number of reads in a fastq file
* downloadFromGenbank.py: Download nucleotide sequences from a list of GenBank acess codes
* phreplace.py: Uses a tab-separated, two column table to find and replace strings in a
text document
* phyles.py: Can change names of multiple files and/or folders. It can also be usefull for
editing text files
* findPrimersForRepeats.py: This program takes a MULTIFASTA file with repetitive DNA
masked (lowercase) with RepeatMasked. It also takes an annotation file in GFF format from
RepeatMasker.
* estimateCopyNumber.py: Histograms from genomeCoverageBed (BED tools) are parsed to
calculate the average coverage of each fragment. Later, the calculation of the number of
copies per repeat follows the following equation: Number of copies = (avg.
coverage/length)/factor The 'factor' is the maximum ratio of average coverage and sequence
length
* MITObim_modified.pl: MITObim script modified for execution in a computer cluster
* outfmt6_to_gtf.py: Converts tables in output format 6 from BALST to GTF (GFF 2)
* parse_annotations.py: Categorize annotations, finding overlaps
* parse_exons.py: reads Sequences and GTF annotations, reporting exons/ CDS
* parseCaf.py: Extract multiple stats from alignment files in CAF format
* selectTiles.py: Helper script for HTQC pipeline
* sudoParallelBlast.py: Template to create PBS scripts for BLAST analyses
* sort_annotations.py: Sort annotations in GTF format according to sequence id

Also includes programs to manage FASTA and FASTQ files:
* pato-fu.py
* fu_checker.py
* fu_counter.py
* fu_deinterleaver.py
* fu_extractor.py
* fu_identifier.py
* fu_interleaver.py
* fu_pruner.py
* fu_randomizer.py
* fu_sorter.py
* fu_suffixes.py
* splitia.py

LICENSE

Copyright (C) 2014—2017 Denis Jacob Machado
GNU General Public License version 3.0
These programs comes with ABSOLUTELY NO WARRANTY.
These are free software, and you are welcome to redistribute it under certain conditions.
For additional information, please visit http://opensource.org/licenses/GPL-3.0

AVAILABILITY

Many of the programs herein are primarily distributed via GitLab. Check my personal
projects at https://gitlab.com/MachadoDJ.

CONTACT

Author: Denis Jacob Machado
Email: machadodj<at>usp.br
Homepage: https://about.me/machadodj