As of December 2024, NCBI's pilot tool, Read assembly and Annotation Pipeline (RAPT) tool will no longer be available. We encourage you to check out NCBI’s suite of assembly and annotation tools including the genome assembler SKESA , the taxonomic assignment tool ANI, and the prokaryotic genome annotation pipeline (PGAP). Learn more
Frequently Asked Questions (FAQs)
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Can I assemble and annotate reads from a virus or fungus using RAPT?
No. RAPT is designed to work on genomic reads sequenced from a single isolate belonging to a bacterial or archaeal species known to NCBI Taxonomy.
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Can I use Nanopore reads, PacBio reads or short reads from sequencing platforms
other than Illumina as RAPT inputs?
No, RAPT currently only accepts reads produced on Illumina sequencing platforms. Reads can be provided to RAPT as FASTQ files or as SRA run accessions (starting with the SRR, DRR or ERR prefix).
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Can I assemble and annotate metagenomic or transcriptomic data using RAPT?
No. RAPT is designed to work on genomic reads sequenced from single isolates from Bacteria or Archaea.
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Can I use reads from SRA as input?
Yes, you can provide an SRA run accession (starting with the SRR, DRR or ERR prefix), using the left (first) box on the home page.
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My reads are not in SRA and are for a paired-end library. What files do I need to
provide as input to RAPT?
You can provide a single FASTQ file, with reads of each pair adjacent to each other (interleaved format), or you can provide two, R1 and R2, files.
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Do adaptor, primer or barcode need to be trimmed, and low quality reads filtered
prior to running RAPT?
No, this is not necessary. SKESA, the assembler used by RAPT, detects high frequency k-mers, marks them as suspect, and uses them to trim reads (see the SKESA publication for more details). Low quality sequences are also unlikely to be incorporated into the assembly because they are unique by nature and therefore represented by k-mers seen once. In RAPT, k-mers encountered only once are not used by the assembly process.
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Does RAPT use the read quality scores in the FASTQ files?
No.
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Does RAPT accept compressed files?
Yes, RAPT accept gzipped files.
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I do not wish to run SKESA. Can I use a different read assembler?
SKESA is the only assembler in RAPT. If you wish to annotate an already assembled genome, please use NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP), which accepts genomes assembled by any assembler.
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How long does a RAPT job take?
The execution time for a job ranges from one to a several hours and depends largely on the size of the genome produced by the first steps of the process. However, a job may not start immediately after submission if no CPU is available. Please contact us at prokaryote-tools@ncbi.nlm.nih.gov if you have not received result after 24 hours.
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How long are my results available for?
RAPT results will be saved for 6 weeks after the job is completed, after which they will be permanently deleted. Please download your results before 6 weeks.
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Can others see my results?
No, unless they know the URL to access them. You and anyone with the URL to the results page can download the data. Therefore, you can choose to share the results with others if you wish, or keep them to yourself.
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I am not confident in the taxonomic classification of the organism I sequenced, so
the scientific name I can provide is only a guess. Is it acceptable?
Yes! The taxonomy check done within RAPT with ANI will derive a scientific name from the best matching assembly in GenBank that is of well-defined origin. Starting in May 2022, the scientific name you provide may be overriden by the scientific name determined by ANI, resulting in a more accurate annotation. The scientific name in the final results is the ANI-chosen name.
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Why is the scientific name in the RAPT results different from the one I specified?
See the question above. If ANI, the step in RAPT that evaluates the taxonomic assignment of the assembly, determines with high confidence that the species that best fits your assembly is different from the name you provided on input, the annotation process will use the ANI-chosen scientific name. If you prefer that the annotation run with the scientific name you have chosen, consider running RAPT at your own institution or in the Cloud with the options of your choice.
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My job failed. Why?
You will receive an email notification if a job failed. Please verify that the inputs your provided are suitable for RAPT. The reads should be Illumina reads from a single bacterial or archaeal genome. Genomic reads from mixed cultures or a metagenomic sample will likely cause failures. If you believe the inputs conform with these requirements, please contact us at prokaryote-tools@ncbi.nlm.nih.gov.
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Is there a limit to the numbers of RAPT jobs I can run?
Yes. Each user is allowed to run 30 jobs per 30-day period. If you wish to run RAPT on a larger scale, please see our GitHub site for running RAPT at your institution or in the Cloud.
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Can I submit RAPT results to GenBank?
No, not yet. If the production of submittable results by RAPT is a feature you'd like us to add, please let us know by emailing prokaryote-tools@ncbi.nlm.nih.gov.
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Is the RAPT web service a new service that I can depend on?
The RAPT web service is a pilot product with limited funding. We cannot guarantee that it will become a production-level product. Your feedback and the usage of the service will be important in deciding the next steps of the project, so please let us know if the service is making a difference in your research.
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Is there any difference in results among RAPT web service, standalone RAPT,
and GCP-RAPT?
No, RAPT web service, standalone RAPT, and GCP-RAPT use the same code but on different platforms.