Release notes, and instructions for installing the programs, are
below. Please note the following:
1. I ask that you not make the programs (including source code,
executables, or any part thereof) available to anyone outside your
group, without first obtaining permission from me. If you are
operating a computer facility which provides access to the programs to
several independent investigators, you should set the permissions on
the executables to allow execute but not read access, so that the
programs may not be copied. Investigators who want copies of the
software for their own use must contact me directly.
2. If you are doing any commercially restricted sequencing, you must
execute a licensing agreement with the University of Washington and
pay a fee in order to use phrap, cross_match, swat, phred, or consed.
"Commercially restricted sequencing" is defined as any sequencing for
which a company retains patenting or licensing rights regarding the
sequence, or the right to restrict or delay dissemination of the
sequence; with the sole exception that sequencing is not considered to
be commercially restricted if it is federally funded AND the
investigators adopt the data release policies endorsed at the Wellcome
Trust-sponsored Bermuda meeting, i.e. immediate release of data as it
is generated. By sending you the software now I am NOT giving you
permission to use it for commercially restricted sequencing. To obtain
the licensing agreement please contact
Gerald B Barnett
Software Technologies Manager
Office of Technology Transfer
University of Washington
Box 354810
1107 NE 45th St, Suite 200
Seattle, WA 98195
206-543-3970
Vmail: 206-685-9972, FAX: 206-685-4767
barnett@u.washington.edu
VERSION 0.960718 RELEASE NOTES:
Version 0.960718 contains the following significant modifications:
1) There have been improvements in memory usage and speed that should
substantially facilitate phrap and cross_match analyses of large
datasets. Cross_match can now be used for database searches.
These changes required a fair amount of reorganization of the
internal data structures. In the course of making them, I have had to
temporarily inactivate the phrap option that allowed one set of reads
to be assembled against a second set of sequences (e.g. reference
sequences being scanned for polymorphisms), using two or more input
files. This will be restored soon.
2) Swat has been improved in several ways. I have restored and
improved its ability to compute z-scores and E values for database
searches, and these now appear to be quite reliable. Also, it is now
possible to use swat for profile searches (with the restriction that
gap penalties still need to be position independent).
3) A graphical viewer for phrap assemblies, "phrapview", is now
included. This is intended to complement the "local" view of the
assembly provided by consed, by giving a "global" view that focusses
on information pertaining to possible incorrectness, incompleteness,
or non-uniqueness of the assembly. Phrapview displays depth of
coverage, forward-reverse read pairs, significant pairwise matches
involving reads in different locations, and chimeric reads. It
requires a ".view" file produced by running phrap with the -view
option. Phrapview is written in perl-tk and to run it you will need to
have installed on your system a recent version of perl that includes
the tk library (available for free from a number of web sites).
Further documentation appears in the file "general.doc". The program
was written rather hastily (in less than a week, including the time to
learn perl and Tk) and I would appreciate any feedback on how to make
it more useful.
4) The following known bugs have been fixed:
(i) A bug that caused occasional crashes in the "Revising contigs" phase.
(ii) Another bug in revise_contigs that occasionally caused premature
truncation of the contig sequence, resulting in massive pileups of
reads at the truncated end; and that also caused a lower quality read
to occasionally be used in place of a higher quality one in deriving
the contig sequence.
(iii) A bug that caused an infinite loop on data readin on SGI
machines (N.B. I don't have access to an SGI computer and so haven't
been able to verify that the programs now run successfully -- please
let me know if there are still problems).
(iv) A bug that caused premature termination of phrap when there are
0 length reads in the dataset.
Please continue to report any bugs to me.
5) Contig base quality information is now output in the .ace file (as
well as the .contigs.qual file). You need to obtain a new version of
consed from David Gordon (which he is distributing this week) in order
to avoid having consed crash on these .ace files. (This version of
consed does not yet actually use the contig base quality information).
6) Phrap, cross_match and swat are now all case insensitive, in the
sense that all sequences are immediately converted to upper case on
readin. The -use_case option is no longer available. If you were
previously using that, you will need to create .qual files that
contain the information instead. In any case (so to speak!) I strongly
recommend that you use phred's quality values which are substantially
more discriminating.
INSTALLATION INSTRUCTIONS:
The email message containing the swat/cross_match/phrap package is in
the form of a uuencoded .tar.Z file; you will need to have access to a
Unix system for the initial unpacking, but once you've uudecoded it
and unpacked the .tar file, you should be able to compile the source
code on computers running other operating systems -- it should be
portable to almost anything with a decent C compiler and adequate
memory (64 Mb RAM or more is desirable). Here are the steps needed to
unpack and install the program:
1) Save that email message as a file (say temp.mail). If possible, do
this using the Unix mail command, rather than another mail program --
some mail programs (e.g. Pine) may remove trailing spaces on each line of
incoming messages, which will corrupt a uuencoded message.
Do not attempt to modify the saved mail message in any way using a
word processor. That is unnecessary and may corrupt the message.
2) To unpack the saved file, execute the following two commands on a Unix
workstation, in the directory containing the file created in (1):
uudecode temp.mail
zcat distrib.tar.Z | tar xvf -
3) To produce working versions of the programs, move (if necessary)
the files produced by the above command to an appropriate computer
having a C compiler, and execute the following command in the
directory containing the files:
make
If your compiler does not recognize the -O2 optimization flag, you
should change the line
CFLAGS= -O2
in the file "makefile" to
CFLAGS= -O
and recompile (this may require removing all executables produced
using the original make).
4) The documentation (which is still somewhat incomplete) is in three
.doc files.
Contact me if you have problems. Before doing so however please
record exactly what steps you carried out, on what computer &
operating system, and what error messages you received.