This software should be available with no extra configuration.
PGA-20230303
General Introduction to PGA
PGA (Plastid Genome Annotator), a standalone command line tool, can perform
rapid, accurate, and flexible batch annotation of newly generated target
plastomes based on well-annotated reference plastomes. In contrast to current
existing tools, PGA uses reference plastomes as the query and unannotated
target plastomes as the subject to locate genes, which we refer to as the
reverse query-subject BLAST search approach. PGA accurately identifies gene
and intron boundaries as well as intron loss. The program outputs
GenBank-formatted files as well as a log file to assist users in verifying
annotations.
We thank Rong Zhang, Ying-Ying Yang and Jian-Jun Jin from Kunming Institute of
Botany Chinese Academy of Sciences, and Pin Gong from Institute of Botany
Chinese Academy of Sciences for improving this tool.
Following six steps will be conducted to annotate plastomes: (1) Preparation
of GenBank-formatted reference plastomes; (2) Preparation of FASTA-formatted
target plastomes; (3) Reference database generation; (4) BLAST search; (5)
Determining feature boundaries; (6) Generating GenBank and log files.
$ PGA.pl -h
Usage:
PGA.pl -r -t [-i -p -q -o -f -l]
Copyright (C) 2020 Xiao-Jian Qu
Please contact <quxiaojian@sdnu.edu.cn>, if you have any bugs or questions.
[-h -help] help information.
[-r -reference] required: (default: reference) input directory name containing GenBank-
formatted file(s) that from the same or close families.
[-t -target] required: (default: target) input directory name containing FASTA-
formatted file(s) that will be annotated.
[-i -ir] optional: (default: 1000) minimum allowed inverted-repeat (IR) length.
[-p -pidentity] optional: (default: 40) any PCGs with a TBLASTN percent identity less
than this value will be listed in the log file and will not be annotated.
[-q -qcoverage] optional: (default: 0.5,2) any PCGs with a query coverage per annotated
PCG less or greater than each of these two values (<1,>1) will be listed
in the log file.
[-o -out] optional: (default: gb) output directory name.
[-f -form] optional: (default: circular) circular or linear form for FASTA-formatted
file.
[-l -log] optional: (default: warning) log file name containing warning information
for annotated GenBank-formatted file(s).
