rnaQUAST: Quality Assessment Tool for Transcriptome Assemblies

Algorithmic Biology Lab in St. Petersburg of SPAdes fame developed a new tool for evaluating quality of transcriptome assemblies using reference genome and annotation (h/t: anton). Stay tuned for more information.

3 Options

3.1 Input data options

To run rnaQuast one needs to provide either FASTA files with transcripts (recommended), or align transcripts to the reference genome manually and provide the resulting PSL files. rnaQUAST also requires reference genome and optionally an annotation.

-r , –reference

Single file with reference genome containing all chromosomes/scaffolds in FASTA format.

-gtf , –annotation

File with annotation in GTF/GFF format.

-c , –transcripts

File(s) with transcripts in FASTA format separated by space.

-psl , –alignment

File(s) with transcripts alignments in PSL format separated by space.

3.2 Basic options

-o , –output_dir

Directory to store all results. Default is rnaQUAST_results/results_.

--test

Run rnaQUAST on the test data from the test_data folder, output directory is rnaOUAST_test_output.

-d, –debug

Report detailed information, typically used only when detecting problems.

-h, –help

Show help message and exit.

3.3 Advanced options

-t , –threads

Maximum number of threads. Default is the number of CPU cores (detected automatically).

-l , –labels

Names of assemblies that will be used in the reports separated by space.

-ss, –strand_specific

Set if transcripts were assembled using strand specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand.

--min_alignment

Minimal alignment size to be used, default value is 50.

--no_plots

Do not draw plots (makes rnaQUAST run a bit faster).