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Sondovač changelog

Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment.

Version 1.X regular release released 2021-MM-DD (WIP)

  • Bug fixes, more robust coding.
  • Updated documentation.
  • Removed colorization of the output, simplified output for user, improved coding standard.
  • Removed build-in software installation.
  • Removed interactive mode, simplified code.

Version 1.3 regular release released 2017-12-18

  • bam2fastq is dropped in favour of samtools fastq. No plans to use Picard anymore (part A).
  • Simplified INSTALL and README not to only copy PDF manual.
  • Corrected output of part A - ensure to have always valid FASTA.
  • Automatically remove putative plastid sequences from final probe set (part B), list of all probes (with putative plastid sequences) and list of putative plastid sequences are available.
  • Updated software distributed with Sondovač, updated respective sections of PDF manual.
  • Removed FASTX Toolkit, conversion from FASTQ to FASTA is done by simple shell function.
  • Improved handling of input/output files when stored in several different directories.
  • Tested with Geneious 10, improved description of Geneious usage in the PDF manual.
  • Improved PDF manual.

Version 1.2 regular release released 2016-06-28

  • Fixed wrong probe design summary statistics (at the end of part B).
  • Added support for Geneious 9.
  • More detailed error reporting (especially in part B).
  • Various smaller fixes.
  • Updated accompanying software to recent versions.

Version 1.1 regular release released 2016-03-15

  • Checking if input FASTA files are interleaved or not (required) and, if needed, FASTA files are converted not to be interleaved.
  • Added requirement of Python.
  • Removed BAM files (part A) - they are not kept anymore.
  • Language checking and enhancements of documentation.
  • Modified CD-HIT-EST.
  • Improved summary of the probe design in part B.
  • More possibilities for minimum total locus length.
  • Various smaller fixes.

Version 1.0 regular release released 2016-01-12

  • Renaming of input FASTA sequences names is required - it ensures correct working of part B.
  • Added check if input files were created on Windows - if so, they are converted into UNIX style EOL.
  • Various smaller fixes.
  • Better showing of the information in part B.
  • Enhanced documentation.

Version 0.99 release candidate released 2015-12-08

  • Fixed error with some input files for part B.
  • Finished colorization of command-line user interface.
  • Added possibility to set minimal exon length of the loci.
  • Various fixes and UI enhancements.
  • Improved documentation.

Version 0.95 beta released 2015-11-27

  • Offer the possibility to choose between transcripts or genome skim sequences for further processing.
  • Colorization of command-line user interface (incomplete).
  • Added possibility to change -minIdentity parameter of BLAT in step 11, part B.
  • Fixed problems with some transcriptome input files.
  • Added possibility to set custom bait length.
  • Added information about article in MER introducing Sondovač.

Version 0.9 beta released 2015-10-23

  • Highly enhanced part B.
  • Better handling of variable output from Geneious.
  • Possibility to specify custom output files name.
  • Full support for Linux distributions using DEB - Debian, Ubuntu, Linux Mint and derivatives.
  • Enhanced documentation.
  • Support for Mac OS X, package management using Homebrew.
  • Support for RedHat based Linux distributions - Fedora, Centos and Scientific Linux and derivatives.
  • Better compilation and installation of required software.
  • For downloading automatically select whether to use wget (preferred) or curl.
  • Various fixes.

Version 0.8 alpha released 2015-10-09

  • Usage of mitochondrial reference sequence is optional.
  • Better formatting of script messages.
  • Various fixes and enhancements.

Version 0.7 alpha released 2015-10-06

  • Fixed reported problems with sed differences among Linux and Mac OS X.
  • Added more exhaustive documentation.
  • Various fixes and enhancements.

Version 0.6 alpha released 2015-08-10

  • Fixed problems with some versions of output of Geneious.
  • Better compilation and installation of required additional software packages.
  • Various fixes and enhancements.

Version 0.5 alpha released 2015-07-24

  • First public release, early alpha stage.