--- name: "sindex" section: "1" platform: "linux" package: "biosquid" version: "1.9g+cvs20050121-15.1+b2" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/sindex" --- # sindex(1) ## NAME - sindex - index a sequence database for sfetch ## SYNOPSIS **sindex** *\[options\]* *seqfile1 \[seqfile2...\]* ## DESCRIPTION **sindex** indexes one or more *seqfiles* for future sequence retrievals by **sfetch.** An SSI ("squid sequence index") file is created in the same directory with the sequence files. By default, this file is called *\.ssi.* If there is more than one sequence file on the command line, the SSI filename will be constructed from the last sequence file name. This may not be what you want; see the *-o* option to specify your own name for the SSI file. *sindex* is capable of indexing large files (\>2 GB) if optional LFS support has been enabled at compile-time. See INSTALL instructions that came with @PACKAGE@. ## OPTIONS - **-h** Print brief help; includes version number and summary of all options, including expert options. - **-o** *\* Direct the SSI index to a file named *\.* By default, the SSI file would go to *\.ssi.* ## EXPERT OPTIONS - **--64** Force the SSI file into 64-bit (large seqfile) mode, even if the seqfile is small. You don't want to do this unless you're debugging. - **--external** Force *sindex* to do its record sorting by external (on-disk) sorting. This is only useful for debugging, too. - **--informat** *\* Specify that the sequence file is definitely in format *\;* blocks sequence file format autodetection. This is useful in automated pipelines, because it improves robustness (autodetection can occasionally go wrong on a perversely malformed file). Common examples include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip; see the printed documentation for a complete list of accepted format names. - **--pfamseq** A hack for Pfam; indexes a FASTA file that is known to have identifier lines in format "\>\[name\] \[accession\] \[optional description\]". Normally only the sequence name would be indexed as a primary key in a FASTA SSI file, but this allows indexing both the name (as a primary key) and accession (as a secondary key). ## SEE ALSO [**afetch**(1)](/afetch/1.md), [**alistat**(1)](/alistat/1.md), [**compalign**(1)](/compalign/1.md), [**compstruct**(1)](/compstruct/1.md), [**revcomp**(1)](/revcomp/1.md), [**seqsplit**(1)](/seqsplit/1.md), [**seqstat**(1)](/seqstat/1.md), [**sfetch**(1)](/sfetch/1.md), [**shuffle**(1)](/shuffle/1.md), [**sreformat**(1)](/sreformat/1.md), [**stranslate**(1)](/stranslate/1.md), [**weight**(1)](/weight/1.md). ## AUTHOR Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. ``` Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu ```