--- name: "asndisc" section: "1" platform: "linux" package: "ncbi-tools-bin" version: "6.1.20170106+dfsg2-6" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/asndisc" --- # asndisc(1) check ASN.1 biological sequence records for discrepancies ## NAME asndisc - check ASN.1 biological sequence records for discrepancies ## SYNOPSIS **asndisc** \[**-**\] \[**-B**\] \[**-C** *N*\] \[**-F**\] \[**-I** *path*\] \[**-L** *str*\] \[**-N** *filename*\] \[**-P** *str*\] \[**-R**\] \[**-S**\] \[**-T**\] \[**-X** *tests*\] \[**-Z**\] \[**-a** *str*\] \[**-b**\] \[**-c**\] \[**-d** *tests*\] \[**-e** *tests*\] \[**-f**\] \[**-i** *filename*\] \[**-k**\] \[**-l**\] \[**-o** *filename*\] \[**-p** *path*\] \[**-r** *dir*\] \[**-s** *ext*\] \[**-t**\] \[**-u**\] \[**-w** *filename*\] \[**-x** *str*\] ## DESCRIPTION **asndisc** is a command-line tool to check ASN.1-format biological sequence records for discrepancies. ## OPTIONS A summary of options is included below. - **-** Print usage message - **-B** Big sequence report - **-C** *N* Max count - **-F** Fix product name list - **-I** *path* Path to Indexed binary ASN.1 data - **-L** *str* Lineage to use - **-N** *filename* File with list of product names to check - **-P** *str* RePort type - g Genome - b Big sequence - m MegaReport - t Include Tag - s Tag for Superuser - **-R** Remote fetching from ID - **-S** Summary report - **-T** Use threads - **-X** *tests* EXpand report categories (comma-delimited list of test names as listed below or ALL). - **-Z** Remote CDS Product Fetch - **-a** *str* ASN.1 type - a Any (default) - e seq-Entry - b Bioseq - s bioseq-Set - m seq-subMit - t baTch bioseq-set - u batch seq-sUbmit - c Catenated seq-entry - **-b** Batch file is Binary - **-c** Batch file is Compressed - **-d** *str* Disable tests (comma-delimited list of test names as listed below). - **-e** *str* Enable tests (comma-delimited list of test names as listed below). - **-f** Use Feature table output format - **-i** *filename* Single input file (standard input by default) - **-k** Local fetching - **-l** Load components in advance - **-o** *filename* Single output file - **-p** *path* Path to ASN.1 files - **-r** *dir* Output directory - **-s** *ext* Output file Suffix (**.dr** by default) - **-t** Big Test Set - **-u** Recurse - **-w** *filename* Suspect product rule filename - **-x** *str* File selection substring (**.sqn** by default) ### AVAILABLE TESTS MISSING\_GENES, EXTRA\_GENES, MISSING\_LOCUS\_TAGS, DUPLICATE\_LOCUS\_TAGS, BAD\_LOCUS\_TAG\_FORMAT, INCONSISTENT\_LOCUS\_TAG\_PREFIX, NON\_GENE\_LOCUS\_TAG, DISC\_COUNT\_NUCLEOTIDES, MISSING\_PROTEIN\_ID, INCONSISTENT\_PROTEIN\_ID, FEATURE\_LOCATION\_CONFLICT, GENE\_PRODUCT\_CONFLICT, DUPLICATE\_GENE\_LOCUS, EC\_NUMBER\_NOTE, PSEUDO\_MISMATCH, JOINED\_FEATURES, OVERLAPPING\_GENES, OVERLAPPING\_CDS, CONTAINED\_CDS, RNA\_CDS\_OVERLAP, SHORT\_CONTIG, INCONSISTENT\_BIOSOURCE, SUSPECT\_PRODUCT\_NAMES, DISC\_PRODUCT\_NAME\_TYPO, DISC\_PRODUCT\_NAME\_QUICKFIX, INCONSISTENT\_SOURCE\_DEFLINE, PARTIAL\_CDS\_COMPLETE\_SEQUENCE, EC\_NUMBER\_ON\_UNKNOWN\_PROTEIN, TAX\_LOOKUP\_MISSING, TAX\_LOOKUP\_MISMATCH, SHORT\_SEQUENCES, SUSPECT\_PHRASES, DISC\_SUSPICIOUS\_NOTE\_TEXT, COUNT\_TRNAS, FIND\_DUP\_TRNAS, FIND\_BADLEN\_TRNAS, FIND\_STRAND\_TRNAS, COUNT\_RRNAS, FIND\_DUP\_RRNAS, RNA\_NO\_PRODUCT, TRANSL\_NO\_NOTE, NOTE\_NO\_TRANSL, TRANSL\_TOO\_LONG, CDS\_TRNA\_OVERLAP, COUNT\_PROTEINS, DISC\_FEAT\_OVERLAP\_SRCFEAT, MISSING\_GENPRODSET\_PROTEIN, DUP\_GENPRODSET\_PROTEIN, MISSING\_GENPRODSET\_TRANSCRIPT\_ID, DISC\_DUP\_GENPRODSET\_TRANSCRIPT\_ID, DISC\_PERCENT\_N, N\_RUNS, ZERO\_BASECOUNT, ADJACENT\_PSEUDOGENES, DISC\_LONG\_NO\_ANNOTATION, NO\_ANNOTATION, DISC\_INFLUENZA\_DATE\_MISMATCH, DISC\_SHORT\_INTRON, DISC\_MISSING\_VIRAL\_QUALS, DISC\_SRC\_QUAL\_PROBLEM, DISC\_MISSING\_SRC\_QUAL, DISC\_DUP\_SRC\_QUAL, DISC\_DUP\_SRC\_QUAL\_DATA, DISC\_HAPLOTYPE\_MISMATCH, DISC\_FEATURE\_MOLTYPE\_MISMATCH, DISC\_CDS\_WITHOUT\_MRNA, DISC\_EXON\_INTRON\_CONFLICT, DISC\_FEATURE\_COUNT, DISC\_SPECVOUCHER\_TAXNAME\_MISMATCH, DISC\_GENE\_PARTIAL\_CONFLICT, DISC\_FLATFILE\_FIND\_ONCALLER, DISC\_CDS\_PRODUCT\_FIND, DISC\_DUP\_DEFLINE, DUP\_DISC\_ATCC\_CULTURE\_CONFLICT, DISC\_USA\_STATE, DISC\_INCONSISTENT\_MOLTYPES, DISC\_SUBMITBLOCK\_CONFLICT, DISC\_POSSIBLE\_LINKER, DISC\_TITLE\_AUTHOR\_CONFLICT, DISC\_BAD\_GENE\_STRAND, DISC\_MAP\_CHROMOSOME\_CONFLICT, DISC\_RBS\_WITHOUT\_GENE, DISC\_CITSUBAFFIL\_CONFLICT, DISC\_REQUIRED\_CLONE, DISC\_SOURCE\_QUALS\_ASNDISC, DISC\_mRNA\_ON\_WRONG\_SEQUENCE\_TYPE, DISC\_RETROVIRIDAE\_DNA, DISC\_CHECK\_AUTH\_CAPS, DISC\_CHECK\_RNA\_PRODUCTS\_AND\_COMMENTS, DISC\_MICROSATELLITE\_REPEAT\_TYPE, DISC\_MITOCHONDRION\_REQUIRED, DISC\_UNPUB\_PUB\_WITHOUT\_TITLE, DISC\_QUALITY\_SCORES, DISC\_INTERNAL\_TRANSCRIBED\_SPACER\_RRNA, DISC\_PARTIAL\_PROBLEMS, DISC\_BACTERIAL\_PARTIAL\_NONEXTENDABLE\_PROBLEMS, DISC\_BACTERIAL\_PARTIAL\_NONEXTENDABLE\_EXCEPTION, DISC\_SUSPECT\_RRNA\_PRODUCTS, DISC\_SUSPECT\_MISC\_FEATURES, DISC\_BACTERIA\_MISSING\_STRAIN, DISC\_MISSING\_DEFLINES, DISC\_MISSING\_AFFIL, DISC\_BACTERIA\_SHOULD\_NOT\_HAVE\_ISOLATE, DISC\_BACTERIA\_SHOULD\_NOT\_HAVE\_MRNA, DISC\_CDS\_HAS\_NEW\_EXCEPTION, DISC\_TRINOMIAL\_SHOULD\_HAVE\_QUALIFIER, DISC\_METAGENOMIC, DISC\_METAGENOME\_SOURCE, ONCALLER\_GENE\_MISSING, ONCALLER\_SUPERFLUOUS\_GENE, DISC\_SHORT\_RRNA, ONCALLER\_CHECK\_AUTHORITY, ONCALLER\_CONSORTIUM, ONCALLER\_STRAIN\_CULTURE\_COLLECTION\_MISMATCH, ONCALLER\_MULTISRC, ONCALLER\_MULTIPLE\_CULTURE\_COLLECTION, DISC\_SEGSETS\_PRESENT, DISC\_NONWGS\_SETS\_PRESENT, DISC\_FEATURE\_LIST, DISC\_CATEGORY\_HEADER, DISC\_MISMATCHED\_COMMENTS, DISC\_STRAIN\_TAXNAME\_MISMATCH, DISC\_HUMAN\_HOST, DISC\_BAD\_BACTERIAL\_GENE\_NAME, TEST\_BAD\_GENE\_NAME, ONCALLER\_ORDERED\_LOCATION, ONCALLER\_COMMENT\_PRESENT, ONCALLER\_DEFLINE\_ON\_SET, ONCALLER\_HIV\_RNA\_INCONSISTENT, SHORT\_PROT\_SEQUENCES, TEST\_EXON\_ON\_MRNA, TEST\_HAS\_PROJECT\_ID, ONCALLER\_HAS\_STANDARD\_NAME, ONCALLER\_MISSING\_STRUCTURED\_COMMENTS, DISC\_REQUIRED\_STRAIN, MISSING\_GENOMEASSEMBLY\_COMMENTS, DISC\_BACTERIAL\_TAX\_STRAIN\_MISMATCH, TEST\_CDS\_HAS\_CDD\_XREF, TEST\_UNUSUAL\_NT, TEST\_LOW\_QUALITY\_REGION, TEST\_ORGANELLE\_NOT\_GENOMIC, TEST\_UNWANTED\_SPACER, TEST\_ORGANELLE\_PRODUCTS, TEST\_SP\_NOT\_UNCULTURED, TEST\_BAD\_MRNA\_QUAL, TEST\_UNNECESSARY\_ENVIRONMENTAL, TEST\_UNNECESSARY\_VIRUS\_GENE, TEST\_UNWANTED\_SET\_WRAPPER, TEST\_MISSING\_PRIMER, TEST\_UNUSUAL\_MISC\_RNA, TEST\_AMPLIFIED\_PRIMERS\_NO\_ENVIRONMENTAL\_SAMPLE, TEST\_DUP\_GENES\_OPPOSITE\_STRANDS, TEST\_SMALL\_GENOME\_SET\_PROBLEM, TEST\_OVERLAPPING\_RRNAS, TEST\_MRNA\_SEQUENCE\_MINUS\_STRAND\_FEATURES, TEST\_TAXNAME\_NOT\_IN\_DEFLINE, TEST\_COUNT\_UNVERIFIED, SHOW\_TRANSL\_EXCEPT, SHOW\_HYPOTHETICAL\_CDS\_HAVING\_GENE\_NAME, TEST\_DEFLINE\_PRESENT, TEST\_MRNA\_OVERLAPPING\_PSEUDO\_GENE, FIND\_OVERLAPPED\_GENES, DISC\_BIOMATERIAL\_TAXNAME\_MISMATCH, DISC\_CULTURE\_TAXNAME\_MISMATCH, DISC\_CHECK\_AUTH\_NAME, NON\_RETROVIRIDAE\_PROVIRAL, RNA\_PROVIRAL, SHORT\_SEQUENCES\_200, DISC\_10\_PERCENTN, N\_RUNS\_14, MOLTYPE\_NOT\_MRNA, TECHNIQUE\_NOT\_TSA, MISSING\_STRUCTURED\_COMMENT, MISSING\_PROJECT, MULTIPLE\_CDS\_ON\_MRNA, DUP\_DISC\_CBS\_CULTURE\_CONFLICT, DIVISION\_CODE\_CONFLICTS, RRNA\_NAME\_CONFLICTS, EUKARYOTE\_SHOULD\_HAVE\_MRNA, MRNA\_SHOULD\_HAVE\_PROTEIN\_TRANSCRIPT\_IDS, ONCALLER\_COUNTRY\_COLON, ONCALLER\_BIOPROJECT\_ID, ONCALLER\_STRAIN\_TAXNAME\_CONFLICT, ONCALLER\_MORE\_NAMES\_COLLECTED\_BY, ONCALLER\_MORE\_OR\_SPEC\_NAMES\_IDENTIFIED\_BY, ONCALLER\_SUSPECTED\_ORG\_IDENTIFIED, ONCALLER\_SUSPECTED\_ORG\_COLLECTED, ONCALLER\_SWITCH\_STRUCTURED\_COMMENT\_PREFIX, DISC\_CITSUB\_AFFIL\_DUP\_TEXT, ONCALLER\_DUPLICATE\_PRIMER\_SET, END\_COLON\_IN\_COUNTRY, DISC\_PROTEIN\_NAMES, DISC\_TITLE\_ENDS\_WITH\_SEQUENCE, DISC\_INCONSISTENT\_STRUCTURED\_COMMENTS, DISC\_INCONSISTENT\_DBLINK, DISC\_INCONSISTENT\_MOLINFO\_TECH, DISC\_GAPS, DISC\_BAD\_BGPIPE\_QUALS, TEST\_SHORT\_LNCRNA, TEST\_TERMINAL\_NS, TEST\_ALIGNMENT\_HAS\_SCORE, UNCULTURED\_NOTES\_ONCALLER, SEQ\_ID\_PHRASES, NO\_PRODUCT\_STRING ## AUTHOR The National Center for Biotechnology Information. ## SEE ALSO [**asnval**(1)](/asnval/1.md), [**cleanasn**(1)](/cleanasn/1.md).