About RAPT
Run RAPT
- Go to the RAPT Home page
- Log in using the Log in button at the bottom of the "Try it!" section.
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Provide Illumina sequencing reads as an SRA run or as FASTQ file(s):
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SRA run
Enter the SRA accession in the box named "Run RAPT with a SRA accession". An example of SRA run is SRR8602029.
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FASTQ file(s)
- Use the box “Run RAPT with unassembled FASTQ file(s)” if submitting file(s) of sequencing reads. Gzipped files are acceptable.
- Enter the organism name (genus only or genus species known to NCBI Taxonomy) in the "Organism" field. You can optionally enter a strain name in the “Strain” field.
- Click “One file” if all reads for the run are in a single file. This file can contain single-end reads or paired-end reads with reads of a pair adjacent to each other in the file (interleaved). Upload the sequencing reads using the "Choose file" button.
- Click “Two files” to provide reads from a paired-end library in two separate, R1 and R2 files. Upload the R1 and R2 files using the "Choose R1 File" and "Choose R2 File" buttons.
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SRA run
- Click the "Submit" button to start RAPT.
- Monitor your email for confirmation that the job has started.
- Another email will inform you when the job is complete. Note that RAPT may take several hours to finish. You can check the status of all your RAPT jobs by clicking on Job List at the top of the page.
- Download RAPT results using the link sent by email or click on the Download icon in the Action column of the Job List table. Note that the results will be deleted after 6 weeks from the time the job was run.
- You can share your results by forwarding to others the URL for the job results you received by email, or by clicking the 'Share' icon in the Job List table.
The Job List table
Review the results
The results of each job are provided as a compressed (gzipped) directory containing the files listed below. These results are available for six weeks after the start date of the job. After six weeks, the data will be deleted from our servers. You can view and download an example set of results here .
Assembly results
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skesa.out.fa:
multi-fasta file of the assembled contigs produced by SKESA
e.g. A snippet of skesa.out.fa file
>Contig_1_122.654 AAAAAAAATAAAAATTTCTTACTTGATTTAATGTTTAATAATAAAAACGGAGACACTTTAATTAAAGATGGTGTTCCAAAAGACTATAAGGTTGCTGATAAAAGTGGTCAAGCAATAACATATGCTTCTAGAAATGATGTTGCTTTTGTTTATCCTAAGGGCCAATCTGAACCTATTGTTTTAGTCATTTTTACGAATAAAGACAATAAAAGTG >Contig_2_109.048 AAAAGGAGATAACAGCATGAGGAGATTACTCAGTCTATTACTAGCTAGTACAATGATTTTAGTCGCATGTGGGAATGCTAACAATGAAAATAAGAAAAAGGAAGACGAAAAAAAATCAGAAGTAAAAAAAGAAGCTAAGAAAAATAATGATAAACCAAAGAACGAAAAGAAGAATCAAGATATAAATAAAAACAATAATGAGCAAGT - assembly_stat_report.tsv: assembly statistics (contig count, base count, min contig length, max contig length, contig N50, contig L50)
Taxonomy verification
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ani-tax-report.txt: results of the
taxonomy check on the assembled sequences reported by the
Average Nucleotide Identity tool
The possible statuses of the verification are:
- CONFIRMED: The organism name associated with the input reads, and assigned to the genome, has been confirmed by ANI. The submitted genus matches the genus of the ANI-predicted organism.
- MISASSIGNED: The organism has been found to be misassigned to the genome. The submitted genus does not match the genus of the ANI-predicted organism.
- INCONCLUSIVE: The organism cannot be identified (due to lack of a close enough type assembly in GenBank)
- CONTAMINATED: The genome is contaminated with sequences from an organism other than the submitted organism
ANI report for assembly: my_gc_assm_name Submitted organism: Staphylococcus aureus (taxid = 1280, rank = species, lineage = Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus) Predicted organism: Staphylococcus aureus (taxid = 1280, rank = species, lineage = Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus) Submitted organism has type: Yes Status: CONFIRMED Confidence: HIGH 97.145 (93.4 90.6) 11348628 assembly Staphylococcus aureus (GCA_006364675.1, ASM636467v1) 97.145 (93.4 90.8) 10960368 assembly Staphylococcus aureus subsp. aureus (GCA_006094915.1, ASM609491v1) 97.145 (93.4 90.8) 1806888 assembly Staphylococcus aureus subsp. aureus DSM 20231 (GCA_001027105.1, ASM102710v1) 97.136 (93.4 90.7) 8986608 assembly Staphylococcus aureus (GCA_900706775.1, 27323_B01) 97.142 (93.4 91.6) 2490008 assembly Staphylococcus aureus subsp. aureus DSM 20231 (GCA_000330825.2, SASA1.0) 97.150 (92.9 92.3) 2855328 assembly Staphylococcus aureus subsp. aureus NBRC 100910 (GCA_001544175.1, ASM154417v1) 97.351 (87.6 92.0) 5947508 assembly Staphylococcus aureus subsp. anaerobius (GCA_002902425.1, ASM290242v1) 88.825 (89.9 87.3) 8121888 assembly Staphylococcus schweitzeri (GCA_900636685.1, 43874_A01) 88.803 (89.7 88.5) 5947498 assembly Staphylococcus schweitzeri (GCA_002902405.1, ASM290240v1) 87.804 (88.3 85.5) 6994448 assembly Staphylococcus argenteus (GCA_900457475.1, 43781_H01) 87.804 (88.3 85.7) 318468 assembly Staphylococcus argenteus (, ) 87.776 (88.3 86.5) 5946738 assembly Staphylococcus argenteus (GCA_002901785.1, ASM290178v1) 82.319 (29.8 30.5) 4960228 assembly Staphylococcus simiae (GCA_900187055.1, 50377_D01) 82.330 (29.7 30.9) 5947108 assembly Staphylococcus simiae (GCA_002902085.1, ASM290208v1) 82.390 (29.0 30.3) 318828 assembly Staphylococcus simiae CCM 7213 = CCUG 51256 (GCA_000235645.2, ASM23564v1) 81.146 (15.7 17.5) 8121238 assembly Staphylococcus warneri (GCA_900636385.1, 41665_E01) 81.124 (15.7 17.6) 5946698 assembly Staphylococcus warneri (GCA_002901765.1, ASM290176v1) 81.894 (13.9 15.2) 8129748 assembly Staphylococcus saccharolyticus (GCA_003970495.1, ASM397049v1) 81.626 (10.9 12.1) 5947578 assembly Staphylococcus hominis subsp. novobiosepticus (GCA_002902465.1, ASM290246v1) 81.655 (10.8 11.8) 5947688 assembly Staphylococcus petrasii subsp. petrasii (GCA_002902565.1, ASM290256v1) -
ani-tax-report.xml:
same as above, in XML format
e.g. A snippet of ani-tax-report.xml file.
<?xml version="1.0"?> <tax-check class="ANI Analysis" assembly="my_gc_assm_name"> <results status="CONFIRMED" confidence="HIGH"> <submitted-taxid taxid="1280" rank="species" org-name="Staphylococcus aureus" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" has-reference="Y"/> <predicted-taxid taxid="1280" rank="species" org-name="Staphylococcus aureus" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="HIGH"/> <join-at-taxid taxid="1280" rank="species" org-name="Staphylococcus aureus" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus"/> <other-taxid taxid="1654388" rank="species" org-name="Staphylococcus schweitzeri" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="LOW"/> <other-taxid taxid="985002" rank="species" org-name="Staphylococcus argenteus" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="LOW"/> <other-taxid taxid="308354" rank="species" org-name="Staphylococcus simiae" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="LOW"/> <other-taxid taxid="33028" rank="species" org-name="Staphylococcus saccharolyticus" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="LOW"/> <other-taxid taxid="1276936" rank="species" org-name="Staphylococcus petrasii" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="LOW"/> <other-taxid taxid="1290" rank="species" org-name="Staphylococcus hominis" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="LOW"/> <other-taxid taxid="1292" rank="species" org-name="Staphylococcus warneri" lineage="Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus" confidence="LOW"/> </results> <data> //////////////////////////////////////////
PGAP annotation results in the following formats:
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annot.gbk:
annotated genome in GenBank flat file format
e.g. A snippet of annot.gbk file
LOCUS Contig_10_70.9703 3418 bp DNA linear BCT 13-NOV-2020 DEFINITION Staphylococcus aureus, whole genome shotgun sequence. ACCESSION VERSION DBLINK Sequence Read Archive: SRR8602029 KEYWORDS WGS. SOURCE Staphylococcus aureus ORGANISM Staphylococcus aureus Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus. REFERENCE 1 (bases 1 to 3418) AUTHORS NCBI,R. TITLE Direct Submission JOURNAL Submitted (13-NOV-2020) Health and Human Service, National Library of Medicine, 8600 Rockville Pike, Bethesda, Maryland 20894, USA COMMENT The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/ ##Genome-Annotation-Data-START## Annotation Provider :: National Library of Medicine Annotation Date :: 11/13/2020 19:16:17 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision :: 2020-09-24.build4894 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total) :: 2,697 CDSs (total) :: 2,628 Genes (coding) :: 2,555 CDSs (with protein) :: 2,555 Genes (RNA) :: 69 rRNAs :: 2, 3, 4 (5S, 16S, 23S) complete rRNAs :: 1 (5S) partial rRNAs :: 1, 3, 4 (5S, 16S, 23S) tRNAs :: 56 ncRNAs :: 4 Pseudo Genes (total) :: 73 CDSs (without protein) :: 73 Pseudo Genes (ambiguous residues) :: 0 of 73 Pseudo Genes (frameshifted) :: 44 of 73 Pseudo Genes (incomplete) :: 18 of 73 Pseudo Genes (internal stop) :: 18 of 73 Pseudo Genes (multiple problems) :: 7 of 73 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..3418 /organism="Staphylococcus aureus" /mol_type="genomic DNA" /db_xref="taxon:1280" gene <1..285 /locus_tag="pgaptmp_000001" CDS <1..285 /locus_tag="pgaptmp_000001" /inference="COORDINATES: similar to AA sequence:RefSeq:YP_499118.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="LPXTG cell wall anchor domain-containing protein" /protein_id="extdb:pgaptmp_000001" /translation="SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDAGKHTPVKPM SATKDHHKKAKALPETGSENNGSNNATLFGGLFAALGSLLLFGRRKKQNK" gene 680..>3418 /locus_tag="pgaptmp_000002" CDS 680..>3418 /locus_tag="pgaptmp_000002" /inference="COORDINATES: similar to AA /////////////////////////////// -
annot.gff:
annotated genome in GFF3 format
e.g. A snippet of annot.gff file
##gff-version 3 #!gff-spec-version 1.21 #!processor NCBI annotwriter ##sequence-region 1 3418 ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1280 Contig_10_70.9703 Local region 1 3418 . + . ID=Contig_10_70.9703:1..3418;Dbxref=taxon:1280;gbkey=Src;mol_type=genomic DNA Contig_10_70.9703 . gene 1 285 . + . ID=gene-pgaptmp_000001;Name=pgaptmp_000001;gbkey=Gene;gene_biotype=protein_coding;locus_tag=pgaptmp_000001;partial=true;start_range=.,1 Contig_10_70.9703 Protein Homology CDS 1 285 . + 0 ID=cds-pgaptmp_000001;Parent=gene-pgaptmp_000001;Name=extdb:pgaptmp_000001;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq :YP_499118.1;locus_tag=pgaptmp_000001;partial=true;product=LPXTG cell wall anchor domain-containing protein;protein_id=extdb:pgaptmp_000001;start_range=.,1;transl_table=11 Contig_10_70.9703 . gene 680 3418 . + . ID=gene-pgaptmp_000002;Name=pgaptmp_000002;end_range=3418,.;gbkey=Gene;gene_biotype=protein_coding;locus_tag=pgaptmp_000002;partial=true Contig_10_70.9703 Protein Homology CDS 680 3418 . + 0 ID=cds-pgaptmp_000002;Parent=gene-pgaptmp_000002;Name=extdb:pgaptmp_000002;end_range=3418,.;gbkey=CDS;inference=COORDINATES: similar to A A sequence:RefSeq:WP_047430389.1;locus_tag=pgaptmp_000002;partial=true;product=fibrinogen-binding adhesin SdrG C-terminal domain-containing protein;protein_id=extdb:pgaptmp_000002;transl_table=11 //////////////////////////////// -
annot.sqn:
annotated genome in ASN format
e.g. A snippet of annot.sqn file
Seq-submit ::= { sub { contact { contact { name name { last "RAPT", first "NCBI" }, affil std { affil "National Library of Medicine", div "Health and Human Service", city "Bethesda", sub "Maryland", country "USA", street "8600 Rockville Pike", email "info@ncbi.nlm.nih.gov", phone "301-594-5983", postal-code "20894" } } }, cit { authors { names std { { name name { last "NCBI", first "RAPT", initials "R." } } }, affil std { affil "National Library of Medicine", div "Health and Human Service", city "Bethesda", sub "Maryland", country "USA", street "8600 Rockville Pike", email "info@ncbi.nlm.nih.gov", phone "301-594-5983", postal-code "20894" } }, date std { year 2020, month 11, day 13, hour 17, minute 50, second 36 } } }, data entrys { set { class genbank, descr { comment "The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/", user { type str "StructuredComment", data { { label str "StructuredCommentPrefix", data str "##Genome-Annotation-Data-START##" }, { label str "Annotation Provider", data str "National Library of Medicine" }, --More--(0%) ///////////////////////////////////////////// -
annot.faa:
multi-fasta file of the proteins annotated on the genome
e.g. A snippet of annot.faa file
>gnl|extdb|pgaptmp_000001 LPXTG cell wall anchor domain-containing protein, partial [Staphylococcus aureus] SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDAGKHTPVKPMSATKDHHKKAKALPETGSENNGSNNA TLFGGLFAALGSLLLFGRRKKQNK >gnl|extdb|pgaptmp_000002 fibrinogen-binding adhesin SdrG C-terminal domain-containing protein, partial [Staphylococcus aureus] MINRDNKKAITKKGMISNRLNKFSIRKYTVGTASILVGTTLIFGLGNQEAKAAENTSTENAKQDDATTSD NKEVVSETENNSTTENNLTNPIKKETNTDSQQEAKEAPTTSSTQQQQNNATTSTETRPQNIEKENVQPST DKTATEDTSVILEEKKAPNNTNNDVTTKPSTSEIQTTPTTPQESTKIENSQPQATPSKVDNQVTDATNPK ESVNVSKEELKNNPEKLKELVRNDSNTDRSTKPVAIAPTSVTPKRVNAKMRFAVAQPAAVASNNVNDLIK VTKQTIKVGDDEDNVVSAHDGEEIEYDSEFTIDNKVKAGDTMTINYDKNVIPSDLTDKNDPIDITDPSGE VIAKGTFDKATKQITYTFTDYVDKYEDIKSRLTLYSYIDKKTVPNETSLNLTFATAGKETNQNVTVDYQD PMVHGDSNIQSIFTKLDEDKQTIEQQIYVNPLKKTATNTKVDIAGSQVDDYGNIKLGNGSTIIDQNTEIK VYKVNPNQQLPQSNRIYDFSQYEDVTSQFDNKKSFSNNVATLDFGDINSAYIIKVVSKYTPTSDGELDIA QGTSMRTTDKYGYYNYAGYSNFIVTSNDTGGGDGTVKPEEKLYKIGDYVWEDVDKDGVQGTDSKEKPMAN VLVTLTYPDGTTKSVRTDANGHYEFGGLKDGETYTVKFETPAGYLPTKENGTTDGEKDSNGSSITVKING KDDMSLDTGFYKEPKYNLGDYVWEDTNKDGIQDANEPGIKDVKVTLKDSTGKVIGTTTTDASGKYKFTDL DNGNYTVEFETPAGYTPTVKNTTAEDKDSNGLTTTGVIKDADNMTLDSGFYKTPKYSLGDYVWYDSNKDG KQDTTEKGIKDVTVTLQNEKGEVIGTTKTDENGKYRFDNLDSGKYKVIFEKPAGLTQTGTNTTEDDKDAD GGE >gnl|extdb|pgaptmp_000003 peroxide-responsive transcriptional repressor PerR [Staphylococcus aureus] MSVEIESIEHELEESIASLRQAGVRITPQRQAILRYLISSHTHPTADEIYQALSPDFPNISVATIYNNLR VFKDIGIVKELTYGDSSSRFDFNTHNHYHIICEQCGKIVDFQYPQLNEIERLAQHMTDFDVTHHRMEIYG VCKECQDK /////////////////////////////// - calls.tab: tab-delimited file of the coordinates of vector, adapter, linkers and commonly used primer sequences detected by VecScreen. Columns are: sequence identifier, whether the sequence is partially (M) or entirely made of foreign sequence (X), range of foreign sequence, source of the contamination, source category. The file is empty if no vector contaminant was found.
CheckM completeness results:
- checkm.txt: Annotated assembly completeness and contamination as calculated by CheckM . See a full description of the file format at this location. Note: 1) The CheckM calculation is performed on the proteins produced by PGAP, 2) the set of markers used by CheckM is determined by the species associated with the genome (as provided on input or as overridden by ANI).
Collected usage information
Limitation on usage
Run RAPT on your own machine
Questions
Feedback
Licensing terms
NCBI RAPT CWL
The NCBI RAPT CWL and other code authored by NCBI is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as United States Government employees and thus cannot be copyrighted. This software is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.
Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.
Please cite NCBI in any work or product based on this material.
Third-party tools
The Docker image contains third-party tools distributed under the licensing terms of the respective license holders.
GeneMarkS-2+
GeneMarkS-2+ is distributed as part of RAPT and PGAP with limited rights of use and redistribution from the Georgia Tech Research Corporation. See the full text of the license.
TIGRFAMs
The original TIGRFAMs database was a research project of the J. Craig Venter Institute (JCVI) . TIGRFAMs, short for The Institute for Genomic Research's database of protein families, is a collection of manually curated protein families focusing primarily on prokaryotic sequences. It consists of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) terminology, Enzyme Commission (EC) numbers, gene symbols, protein family names, descriptive text, cross-references to related models in TIGRFAMs and other databases, and pointers to the literature. The work has been described in the articles listed in the References section above and use of the TIGRFAMs database must grant proper attribution by citing those four articles.
As of April 2018, rights were transferred to the National Center for Biotechnology Information (NCBI), National Library of Medicine, NIH, for the data to be made available for distribution under a Creative Commons Attribution-ShareAlike 4.0 license. Please see https://creativecommons.org/licenses/by-sa/4.0/ for a brief summary of the license and https://creativecommons.org/licenses/by-sa/4.0/legalcode to see the full text.
CheckM
GNU General Public License v3.0
Permissions of this strong copyleft license are conditioned on making available complete source code of licensed works and modifications, which include larger works using a licensed work, under the same license. Copyright and license notices must be preserved. Contributors provide an express grant of patent rights. See the full text of the license.
References
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RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F.Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028.
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RefSeq: an update on prokaryotic genome annotation and curationHaft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD.Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860. doi: 10.1093/nar/gkx1068.
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NCBI prokaryotic genome annotation pipeline.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, OstellJ. Nucleic Acids Res. 2016 Aug 19;44(14):6614-24. Epub 2016 Jun 24.
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Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI.Ciufo S, Kannan S, Sharma S, Badretdin A, Clark K, Turner S, Brover S, Schoch CL, Kimchi A, DiCuccio M.Int J Syst Evol Microbiol. 2018 Jul;68(7):2386-2392.
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SKESA: strategic k-mer extension for scrupulous assemblies.Souvorov A, Agarwala R, Lipman D.Genome Biol. 2018 Oct 4; 19(1):153. doi: 10.1186/s13059-018-1540-z.
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Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.Lomsadze A, Gemayel K, Tang S, Borodovsky M.Genome Research. 2018; 28(7):1079-1089.
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TIGRFAMs: a protein family resource for the functional identification of proteins.Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O.Nucleic Acids Res. 2001 Jan 1;29(1):41-3.
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The TIGRFAMs database of protein families.Haft DH, Selengut JD, White O.Nucleic Acids Res. 2003 Jan 1;31(1):371-3.
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TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O.Nucleic Acids Res. 2007 Jan;35 (Database issue):D260-4. Epub 2006 Dec 6.
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TIGRFAMs and Genome Properties in 2013.Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.Nucleic Acids Res. 2013 Jan;41(Database issue): D387-95. doi: 10.1093/nar/gks1234. Epub 2012 Nov 28.
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Rfam 12.0: updates to the RNA families database.Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.Nucleic Acids Res. 2015 Jan;43(Database issue): D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.
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PILER-CR: fast and accurate identification of CRISPR repeats.Edgar RC.BMC Bioinformatics. 2007 Jan 20;8:18.
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CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P.BMC Bioinformatics. 2007 Jun 18;8:209.
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tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.Chan PP, Lowe TM.Methods Mol Biol. 2019;1962:1-14. doi: 10.1007/978-1-4939-9173-0_1
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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomesParks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW.Genome Res. 2015;25(7):1043-1055. doi:10.1101/gr.186072.114