LASTZ Release 1.0.21 built Sep/9/2008

TABLE OF CONTENTS

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

Introduction

This document describes installation and usage of the LASTZ sequence alignment program. LASTZ is a drop-in replacement for BLASTZ, and is backward compatible with BLASTZ's command-line options. That is, it supports all of BLASTZ's options but also has additional ones, and may produce slightly different alignment results.

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

Installation

If you have received the distribution as a packed archive, unpack it by whatever means are appropriate for your computer. The result should be a directory <somepath>/lastz‑distrib‑X.XX.XX that contains a src subdirectory (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 tell the installer where to put the executable, either by setting the shell variable $LASTZ_INSTALL, or by editing the make‑include.mak file to set the definition of installDir. Also, be sure to add the directory you choose to your $PATH.

Then to build the LASTZ executable, enter the following commands from bash (or a similar command-line shell). 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 whether the build succeeded. To run it, enter the following command:

    make test

    make: *** [test] Error 1

Examples

Aligning a human chromosome to a chicken chromosome

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

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

Comparing shotgun reads to a human chromosome

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

Command-Line Options

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

The general format of the LASTZ command line is

    lastz <target_file> <query_file> [<options>]

The target_file and query_file are usually just the names of files containing the two sequences to be aligned, either in FASTA, Nib, or 2Bit format. However they can also specify subsequences from these files; running

    lastz --help=files

For options, the general format is ‑‑<keyword> or ‑‑<keyword>=<value>, but for BLASTZ compatibility some options also have an alternative syntax <letter>=<number>.

Running the command lastz without any arguments prints a help message with the most commonly used options, while 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 shotgun reads (as the query). They are selected based on 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).

Change History