ANNOgesic: Accurate RNA-Seq-based annotation of bacterial and archaeal genomes
Processing and integrating RNA-Seq data in order to generate high-resolution annotations is challenging, time consuming and requires numerous different steps. ANNOgesic is a powerful and modular pipeline that provides the required analyses and simplifies RNA-Seq-based bacterial and archaeal genome annotation. It predicts and annotates numerous features, including small non-coding RNAs, with high precision.
References:
- Sung-Huan Yu, Jörg Vogel and Konrad U.Förstner, 2018.
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes.
GigaScience, DOI:10.1093/gigascience/giy096, PMID:30169674. - Sung-Huan Yu, Jörg Vogel and Konrad Ulrich Förstner,
ANNOgesic: A Pipeline To Translate Bacterial/Archaeal RNA-Seq Data Into High-Resolution Genome Annotations.
bioRxiv preprint first posted online May. 27, 2017; doi: http://dx.doi.org/10.1101/143081i.
Documentation
Important Notes
- Module Name: ANNOgesic (see the modules page for more information)
- Implemented as a Singularity container
- Unusual environment variables set
- AG_HOME ANNOgesic installation directory
- AG_BIN ANNOgesic executable directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=4g [user@cn3316 ~]$ module load ANNOgesic [+] Loading singularity 4.0.1 on cn3316 [+] Loading ANNOgesic 1.1.14 ...At this point, user has two options:
1) typing the command
[user@cn3316 user]$ ag(without arguments) will bring the user into the singularity container shell environment
Singularity ANNOgesic.sqsh:~>from which one can run any script or command accessible within the container on any data accessible from inside the container. For example, the following commands will run built-in tests:
Singularity ANNOgesic.sqsh:~> python /ANNOgesic/tests/test_operon.py Detecting operons of test Warning: No proper file - test.gff .. ---------------------------------------------------------------------- Ran 2 tests in 0.009sTo exit from the container shell environment, type:
Singularity ANNOgesic.sqsh:~> python3 /ANNOgesic/tests/test_plot_PPI.py .......Plotting nusB .. ---------------------------------------------------------------------- Ran 9 tests in 1.567s OK
Singularity ANNOgesic.sqsh:~> exit
2) typing the same command followed by another supported command as an additional aggument will result in performiing the second command without explicitly entering the container shell. For example:
[user@cn3316 ~]$ ag python /ANNOgesic/tests/test_gen_svg.py . ---------------------------------------------------------------------- Ran 1 test in 0.004s OK [user@cn3316 ~]$ ag python3 /ANNOgesic/tests/test_converter.py .......... ---------------------------------------------------------------------- Ran 10 tests in 0.018s OKIn particular, the following command will display ANNOgesic help message:
[user@cn3316 ~]$ ag annogesic --help
___ _ ___ ______ _
/ | / | / / | / / __ \____ ____ _____(_)____ \
__ / /| | / |/ / |/ / / / / __ `/ _ \/ ___/ / ___/__\
| / ___ |/ /| / /| / /_/ / /_/ / __(__ ) / /__ /
| /_/ |_/_/ |_/_/ |_/\____/\__, /\___/____/_/\___/ /
| /____/
|__________________
|_____________________
|________________________________________________
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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 reference genomes if the reference
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
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. ANNOgesic.sh). For example:
#!/bin/bash module load ANNOgesic ag python /ANNOgesic/tests/mock_gff3.py ag python /ANNOgesic/tests/mock_helper.py ag python /ANNOgesic/tests/test_blast_class.py ag python /ANNOgesic/tests/test_change_db_format.py ag python /ANNOgesic/tests/test_check_orphan.py ag python3 /ANNOgesic/tests/test_circRNA.py ag python /ANNOgesic/tests/test_circrna.py ag python /ANNOgesic/tests/test_color_png.py ag python /ANNOgesic/tests/test_combine_frag_tex.py ag python3 /ANNOgesic/tests/test_combine_gff.py ag python /ANNOgesic/tests/test_compare_sRNA_sORF.py ag python3 /ANNOgesic/tests/test_converter.py
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] ANNOgesic.sh