-
Notifications
You must be signed in to change notification settings - Fork 3
/
README
57 lines (40 loc) · 2.43 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
DNA Triangulation: Genome scaffolding from in vivo DNA interaction frequency
----------------------------------------------------------------------------
All code was written by Noam Kaplan, University of Massachusetts Medical School, 2013
For further information contact [email protected]
This project is maintained as a github repository at: http://github.com/NoamKaplan/dna-triangulation/
1. Files:
Makefile (containing examples of how to run the code)
triangulation.py (library containing core functions)
augmentation_chr_pred.py (scaffold augmentation chromosome prediction)
augmentation_locus_pred.py (scaffold augmentation locus prediction)
karyotype.py (de novo karyotyping)
scaffold_chr.py (de novo chromosome scaffolding)
contig_positions.tab (data file containing hg19-mapped positions of Allpaths-LG/GAGE contigs, see Makefile)
README
2. Requirements:
Code was written in Python 2.7.2 on a 64-bit Linux operating system.
The following external Python modules are required: numpy, scipy, scikit-learn.
3. Design notes:
Code was designed such that all triangulation algorithms (augmentation+de novo) are contained in the triangulation.py module,
in addition to some helper functions. Each of the other scripts is executable and interfaces with this module.
Scripts that perform heavy computations have been designed so they can be run in a distributed form either as multiple
processes on a single machine or multiple processes on multiple machines.
Note that some scripts currently require loading large matrices into RAM.
karyotype.py and scaffold_chr.py use randomizations, but utilize seeds for reproducible results.
4. License and citation:
This software is free for non-commercial use. For commercial use, please contact author.
The software may be modified and distributed.
If you find this software useful, please cite:
High-throughput genome scaffolding from in vivo DNA interaction frequency
Noam Kaplan and Job Dekker
Nature Biotechnology, 2013
doi:10.1038/nbt.2768
5. Disclaimer:
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.