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.
3.1 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_.
Run rnaQUAST on the test data from the test_data folder, output directory is rnaOUAST_test_output.
Report detailed information, typically used only when detecting problems.
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.
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.
Minimal alignment size to be used, default value is 50.
Do not draw plots (makes rnaQUAST run a bit faster).