ANNOgesic is the swiss army knife for RNA-Seq based annotation of bacterial/archaeal genomes.
It is a modular, command-line tool that can integrate different types of RNA-Seq data based on dRNA-Seq (differential RNA-Seq) or RNA-Seq protocols that inclusde transcript fragmentation to generate high quality genome annotations. It can detect genes, CDSs/tRNAs/rRNAs, transcription starting sites (TSS) and processing sites, transcripts, terminators, untranslated regions (UTR) as well as small RNAs (sRNA), small open reading frames (sORF), circular RNAs, CRISPR related RNAs, riboswitches and RNA-thermometers. It can also perform RNA-RNA and protein-protein interactions prediction. Furthermore, it groups genes into operons and sub-operons and reveal promoter motifs. It can also allocate GO term and subcellular localization to genes. Several of ANNOgesic features are new implementations while other build on well known third-party tools for which it offers adaptive parameter-optimizations. Additionally, numerous visualization and statistics help the user to quickly evaluat feature predictions resulting from an ANNOgesic analysis. The tool was heavily tested with several RNA-Seq data set from bacterial as well as archaeal samples.
Documentation can be found on here.
If you have all the requirements installed, installation can be done by using pip3.
With root permission:
$ pip3 install ANNOgesic
without root permission
$ pip3 install --user ANNOgesic
If you want to know the requirement, please refer to Documentation.
In order to solve the issue of installing the dependencies, a Docker image of ANNOgesic is provided in Docker Hub. The image can be pulled by using Docker or Singularity. Moreover, the users can build an Docker image from the Dockerfile by themselves. For the details, please check the documentation.
The alternative way for installing ANNOgesic is directly clone the Git repository.
$ git clone https://github.com/Sung-Huan/ANNOgesic.git
or
$ git clone [email protected]:Sung-Huan/ANNOgesic.git
In order to make ANNOgesic runnable, we should create a soft link of annogesiclib in bin.
$ cd ANNOgesic/bin $ ln -s ../annogesiclib .
Then, you can run ANNOgesic via specifying the installed path if all the requirements are setup properly.
usage: annogesic [-h] [--version]
{create,get_input_files,update_genome_fasta,annotation_transfer,
tss_ps,optimize_tss_ps,terminator,transcript,utr,srna,sorf,
promoter,operon,circrna,go_term,srna_target,snp,ppi_network,
localization,riboswitch_thermometer,crispr,merge_features,
screenshot,colorize_screenshot_tracks}
...
positional arguments:
{create,get_input_files,update_genome_fasta,annotation_transfer,tss_ps,
optimize_tss_ps,terminator,transcript,utr,srna,sorf,promoter,operon,circrna,
go_term,srna_target,snp,ppi_network,localization,riboswitch_thermometer,
crispr,merge_features,screenshot,colorize_screenshot_tracks}
commands
create Create a project
get_input_files Get required files. (i.e. annotation files, fasta
files)
update_genome_fasta
Get fasta files of query genomes if the query
sequences do not exist.
annotation_transfer
Transfer the annotations from a closely related
species genome to a target genome.
tss_ps Detect TSSs or processing sites.
optimize_tss_ps Optimize TSSs or processing sites based on manual
detected ones.
terminator Detect rho-independent terminators.
transcript Detect transcripts based on coverage file.
utr Detect 5'UTRs and 3'UTRs.
srna Detect intergenic, antisense and UTR-derived sRNAs.
sorf Detect expressed sORFs.
promoter Discover promoter motifs.
operon Detect operons and sub-operons.
circrna Detect circular RNAs.
go_term Extract GO terms from Uniprot.
srna_target Detect sRNA-mRNA interactions.
snp Detect SNP/mutation and generate fasta file if
mutations were found.
ppi_network Detect protein-protein interactions suported by
literature.
localization Predict subcellular localization of proteins.
riboswitch_thermometer
Predict riboswitches and RNA thermometers.
crispr Predict CRISPR related RNAs.
merge_features Merge all features to one gff file.
screenshot Generate screenshots for selected features using IGV.
colorize_screenshot_tracks
Add color information to screenshots (e.g. useful for
dRNA-Seq based TSS and PS detection. It only works
after running "screenshot" (after running batch
script).
optional arguments:
-h, --help show this help message and exit
--version, -v show version
SH Yu, J. Vogel, KU Förstner. 2018, GigaScience, DOI:10.1093/gigascience/giy096, PMID:30169674.
ISC (Internet Systems Consortium license ~ simplified BSD license) - see LICENSE
If you have any questions, please contact Sung-Huan Yu