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SPOA(1) User Commands SPOA(1)

NAME

spoa - SIMD partial order alignment tool

SYNOPSIS

spoa [options ...] <sequences>

DESCRIPTION

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap).

OPTIONS

<sequences>

input file in FASTA/FASTQ format containing sequences

Optional

-m, --match <int>

default: 5 score for matching bases

-x, --mismatch <int>

default: -4 score for mismatching bases

-g, --gap <int>

default: -8 gap penalty (must be negative)

-l, --algorithm <int>

default: 0 alignment mode:
0 - local (Smith-Waterman) 1 - global (Needleman-Wunsch) 2 - semi-global

-r, --result <int>

default: 0 result mode:
0 - consensus 1 - multiple sequence alignment 2 - 0 & 1

--version

prints the version number

-h, --help

prints the usage

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

June 2018 spoa 1.1.3