jacobjmarks / biosig

Genomic Sequence Indexing/Signature Generation and Searching

BioSig

Genomic Sequence Indexing/Signature Generation and Searching.

A partial revive and simplification of Dr. Timothy Chappell's TopSig, focusing on genomic documents.

Getting Started

Utilising the Makefile, running make will build an executable file biosig that can be used as follows.

Indexing (index)

Generate a signature file from the given sequence file/s.

./biosig index [OPTIONS] sequenceFile [sequenceFile2 [...]] -o outfile.bsig

Available OPTIONS:

Option	Default	Description
-kmerlen	5	Kmer length to hash.
-sigwidth	1024	Signature size in bits.
-sigdensity	0.047619048	Signature density 0-1.
-match	(disabled)	Match and store sequence IDs with the given regular expression. Will prioritise first group () if present.
-q	(disbaled)	Quiet operation; Suppress output.

Indexing will result in the output of both a signature file outfile.bsig, as well as a header file outfile.bsig.head, with the following formats:

Signature File .bsig (continuous binary)

This file contains the signatures that were generated from the sequences.

[signature A][signature B][...]

Header File .head (newline-delimited plaintext)

This file contains the IDs of the sequences that were indexed. The first line contains metadata regarding the indexing parameters.

[kmer length],[signature width],[signature density],[sequence count]
[sequence id A]
[sequence id B]
[...]

Searching (search)

Search/Compare the signatures in a given signature file with one or more query signature files.

./biosig search [OPTIONS] targetSig.bsig querySig.bsig [querySig2.bsig [...]] -o resultfile

Available OPTIONS:

Option	Default	Description
-threshold	0.0	Filter results lower than the given similarity threshold 0-1.
-top	0 (disabled)	Retain only the top k results.
-format	tsv	Result output format. (tsv | csv | trec)
-unique	(disabled)	Do not compare signatures with identical IDs.
-match	(disabled)	Match and store sequence IDs with the given regular expression. Will prioritise first group () if present.
-q	(disbaled)	Quiet operation; Suppress output.

Results will be output as follows, depending on the format:

tsv (tab-separated values)

[query]    [target]    [similarity]

csv (comma-separated values)

[query],[target],[similarity]

trec (Text REtrieval Conference)

[query] Q0 [target] [rank] [similarity] biosig