Assemble E. coli's genome from long reads with high error rate from PacBio
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doc
src
test
.gitignore
CMakeLists.txt
README.mkd
result.fasta
seeds.txt

README.mkd

About

This is a course project of Computational Biology at Stony Brook University. http://www.cs.sunysb.edu/~skiena/549/

The project aims at assembling the long sequences reads with high error rate from PacBio. http://www.pacbiodevnet.com/Share/Datasets/E-coli-Outbreak

More details are available on the documents in doc/.

Install

The program has been built and tested on 32 bit Linux.

$ uname -a
Linux ming-laptop 2.6.32-33-generic #69-Ubuntu SMP ... i686 GNU/Linux
$ gcc -v
gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)

The core code should be portable except the binary format. However, the author only have an old laptop with small memory. IO is slow and painful, so...

Cmake and Googletest are necessary to build and run it. Define an environment variable GOOGLE_TEST to the directory of the Googletest.

$ export GOOGLE_TEST=/path/to/googletest
$ cmake .
$ make
$ make test

Make sure it passes all test cases before you proceed.

Usage

The main program is spaced_seed:

$ src/spaced_seed
usage: src/spaced_seed [options] bin seedfile
options: [-f:r:d:m:t:lh]
   -h          Get help and usage.
   -f file     Use the string from file as starting reference. Only
               the first 2 lines of the file read be read, the 1st
               line is supposed to be the sequence, and the second
               should be an integer represents its weight (large
               integer means more weight).
               Without this option the problem will select a random
               segments as starting reference instead.
   -r ratio    Ratio of difference (0.3 by default) allowed.
   -d dumpfile Dump matched segments.
   -m nround   Maximum number of round of iteration.
   -t ntrials  Number of seeding trial for each segment.
   -l          Lock reference during iteration.

Use src/binary_test to build binary sequnce file from .fasta file:

$ src/binary_test
usage: src/binary_test option filename
options: 0 do in-memory checks for DNA text from stdin
         1 read text input from stdin write to binary file
         2 read binary file write text to stdout

For example,

$ cat test/real_align.txt | src/binary_test 1 toy.bin
$ src/spaced_seed toy.bin seeds.txt

Note: Use at your own risk and DO NOT use it for homeworks!