---
name: "sdpMatcher"
section: "1"
platform: "linux"
package: "blasr"
version: "5.3+0-1"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/sdpMatcher"
---

# sdpMatcher(1)

nucleotide sequence matching using sparse dynamic programming

## NAME

sdpMatcher - nucleotide sequence matching using sparse dynamic programming

## SYNOPSIS

**sdpMatcher** *query* *target* *k* \[**-indelRate** *delta*\] \[**-showalign**\] \[**-printsw**\] \[**-noRefine**\] \[**-indel** *i*\] \[**-local**\] \[**-match** *m*\] \[**-sdpIndel** *i*\]

## DESCRIPTION

Performs sparse dynamic programming (SDP) between pairs of sequences as they  are given in two FASTA files, called *query* and *target* for convenience. *k* is the size of the k-mer used for the SDP algorithm.

## SEE ALSO

[**blasr**(1)](/blasr/1.md) [**loadPulses**(1)](/loadPulses/1.md) [**pls2fasta**(1)](/pls2fasta/1.md) [**samFilter**(1)](/samFilter/1.md) [**samtoh5**(1)](/samtoh5/1.md) [**samtom4**(1)](/samtom4/1.md) [**sawriter**(1)](/sawriter/1.md) [**toAfg**(1)](/toAfg/1.md)