Required tools or databases

Each module has different required tools or databases. For running a module, the users just need to install the specific tools for it. For examples, running TSS prediction only needs TSSpredator.

Please also check our Docker image. Via Docker image, all the required tools and environment can be installed and set automaticaly. Moreover, Singularity can be used for building and running Docker image without root permission.

All the used tools are eithor compatible with the ISC license of ANNOgesic or open source.

Tools

Basic requirement:

Python : version higher or equal to 3.4.

BioPython: version higher or equal to 1.65.

Wget: version higher or equal to 1.17.1.

Matplotlib : version higher or equal to 1.5.0.

NumPy : version higher or equal to 1.9.2.

Annotation transfer:

BioPerl: version higher or equal to 1.6.1.

RATT : version higher or equal to 1.64. Please be attention, before you start to run RATT (annotation transfer), run source $PAGIT_HOME/sourceme.pagit first. It will modify the path for execute RATT. If you run ANNOgesic through Docker container, you can skip this step.

SNP calling:

Samtools : version higher or equal to 1.3.1 (using htslib 1.3.1).

Bcftools : version higher or equal to 1.3.1 (using htslib 1.3.1).

TSS and PS prediction:

TSSpredator : version higher or equal to 1.06.

TSS and PS parameter optimization:

TSSpredator : version higher or equal to 1.06.

sRNA detection:

Blast+ : version higher or equal to 2.2.28+.

ViennaRNA : version higher or equal to 2.3.2. RNAfold, mountain.pl and relplot.pl are needed for sRNA prediction.

Terminator detection:

TranstermHP : version higher or equal to 2.09.

ViennaRNA : version higher or equal to 2.3.2. RNAfold is needed for terminator prediction.

Promoter search:

MEME : version higher or equal to 4.11.1.

GLAM2 : version higher or equal to 4.11.1.

MPICH : version higher or equal to 3.2. It is for parallel version of promoter detection.

sRNA target prediction:

ViennaRNA : version higher or equal to 2.3.2.

RNAup, RNAplex, RNAplfold are required for executing many modules of ANNOgesic.

IntaRNA: version higher or equal to 2.0.4.

Circular RNA detection:

Samtools : version higher or equal to 1.3.1 (using htslib 1.3.1).

Segemehl : version higher or equal to 0.1.9. When you install Segemehl, please type ‘make all’ instead of ‘make’ after running configure. Otherwise, the testrealign.x won’t appear.

Riboswitch and RNA thermometer identification:

Infernal : version higher or equal to 1.1.1.

CRISPR detection:

CRT: version higher or equal to 1.2.

Subcellular localization prediction:

Psortb : version higher or equal to 3.0.

Protein-protein interaction detection:

Networkx : version higher or equal to 1.10.

Generating screenshots of IGV:

Colorization of screenshots:

ImageMagick : version higher or equal to 6.9.0-0.

Databases

sRNA detection:

BSRD (A suggestion for sRNA prediction and can be found here.)

nr database

Riboswitch and RNA thermometer prediction:

Rfam (Only including Rfam IDs of riboswitches and RNA thermometers – the datasets can be found here.)

GO term identification:

Protein-protein interaction detection:

species.v${VERSION}.txt from STRING (${VERSION} represents the version number.)