Changelog

This page contains (mostly) all of the changes that were made between each version of EnTAP. The current latest version is EnTAP Beta v0.8.0-beta

EnTAP Beta v0.8.0-beta

  • Overhaul of the taxonomic/gene ontology databases

    • Faster accession/indexing
    • MUST be re-downloaded and re-indexed (or use the updated versions that come with the EnTAP distribution)
    • Taxonomic database includes thousands more entries with synonyms of many species
    • Perl is no longer a dependency, with Python being used to download the database

  • Added blastx support

    • Blastx now allowed for ALL stages of annotation (similarity search + ontology)
    • –runN flag now specifies blastx (frame selection will not be ran)
    • –runP flag now specifies blastp (frame selection will be performed if nucleotide sequences are input)

  • Added InterProScan support

    • Now possible to run EggNOG and/or InterProScan (with both blastx or blastp)
    • EggNOG and/or InterProScan specified with –ontology flag (0 and/or 1)
    • Full output of both will be provided in the final annotations file

  • Added additional statistics to the log file for EggNOG and Expression Analysis

  • Added numerous file/path/software checks to the start of an EnTAP run

    • Test runs/path checks are performed on all software that will be ran
    • Additional checks to specific flags
    • These checks can be turned off for an EnTAP run with –no-check flag (not advised!)

  • –tag flag changed to –out-dir to specify output directory (not just what you’d like it named as)

    • Defaults to current directory with /outfiles folder

  • –paired-end flag for Expression Filtering changed to –single-end (with paired-end being the default)

  • Added contaminant and informative yes/no columns in final annotations file (among other headers)

  • Added ability to input your own list of informative/uninformative terms for EnTAP to flag

  • Added contaminant and none contaminant final annotation files

  • Fixed a sequence id issue in Expression Filtering not mapping to BAM/SAM file

  • Fixed a bug in –trim flag for sequence headers

  • Fixed a bug where some systems had issues with graphing

  • Debug and log files are now time stamped and not overwritten

  • Fixed pathing for EnTAP configuration and made more streamlined

  • Fixed several instances of older compilers complaining

  • Added a lot of error messaging to help diagnose any issues easily

  • Changed similarity search to have full database name, not path

  • Fixed a bug in parsing input fasta file (added corrupt file checks)

EnTAP Beta v0.7.4.1-beta

  • Minor changes to taxonomic database download and indexing

EnTAP Beta v0.7.4-beta

  • Initial beta release!