LASTZ

TABLE OF CONTENTS

• Introduction
• Installation
• Examples
• Command-Line Options
  • Commonly-Used Options
  • Yasra-Specific Options

Introduction

LASTZ -- Tool for (1) Pairwise DNA sequence alignment and (2) alignment scores inference.

This is a preliminary document, covering installation, common options, and support for yasra. A more detailed document decribing additional features is forthcoming.

Installation

If you have received the distribution as a packed archive, unpack the archive by whatever means are appropriate for your computer. The result should be a directory <somepath>/lastz-distrib-X.XX.XX that contains a src subdirectories (and some others). You may find it convenient to remove the revision number (-X.XX.XX) from the directory name. Before building or installing any of the programs, you will need to do one of two things. Either create the shell variable

    $LASTZ = <somepath>/lastz-distrib-X.XX.XX

    <somepath>/lastz-distrib-X.XX.XX/make-include.mak

Then to build the LASTZ executable, from bash (or a similar command line shell), do the commands below. This will build two executables (lastz and lastz_D) and copy them into your installDir.

    cd <somepath>/lastz-distrib-X.XX.XX/src
    make
    make install

A simple self test is included so you can test that the build succeeded. To run it, do this command:

    make test

    make: *** [test] Error 1

Examples

Aligning a human chromosome to a chicken chromosome

To run a quick low-sensititivy alignment of these sequences:

    lastz hg18.chr4 galGal3.chr4 C=3 T=2 Z=10 --maf > hg18_4.galGal3_4.maf

Comparing shotgun reads to a human chromosome

    lastz hg18.chr22 reads --yasra98 --maf > hg18_22.reads.maf

Command-Line Options

If you are familiar with BLASTZ, you can run LASTZ the same as you ran BLASTZ, with the same options and input files. In addition to BLASTZ compatibility, LASTZ provides other options.

The general format of the LASTZ command line is

    lastz target_file query_file options

    lastz ‑‑help=files

The general format for options is ‑‑<name> or ‑‑<name>=<value>. For BLASTZ compatibility some options can be set with <letter>=<number>.

Running the command lastz without specifiers or options gives a list of the most commonly used options. Running

    lastz ‑‑help

Commonly-Used Options

Yasra-Specific Options

There are several options to support the yasra mapping assembler. These provide canned sets of option settings that work well for aligning an assembled reference sequence (as the target) with a set of shortgun reads (as the query). The option relate to the expected level of identity between the sequences. For example, ‑‑yasra90 should be used when we expect 90% identity. The ‑‑yasraXXshort options are appropriate when the reads are very short (less than 50 bp).