|
|
|
||||||||||
New: Interdisciplinary PhD Program Systems Biology
Open Positions
Assistant Professor (Tenure Track) of Micro- or Nanofluidics
(Senior) Postdoc and PhD Student Positions in Synthetic Biology
Postdoc Opening in Micro- or Nanofluidics and Single-Cell Handling/Analysis
Scientist / Engineer at the Single Cell Unit (SCU)
Senior Software Engineer for CISD (Center for Information Services and Databases)
Department Seminar Series
Next Seminar: Tuesday, November 24, 4.00 pm
Marco Vignuzzi, Pasteur Institute Paris
RNA Virus Quasispecies Dynamics:
Linking polymerase fidelity, mutation
frequencies and pathogenesis
Antrittsvorlesungen:
Montag, 7. Dezember 2009
Prof. Dagmar Iber
Computational Biology Group, D-BSSE
Biologie und Banking - Mathematische Verbindungen
17.15 Uhr im ETH Zentrum HG F 30
News from ETH Zürich
| Instead making complicated folds in sheet metal to give it strength, two ETH Zurich architects simply inflate the space between sheet metal shapes. Thanks to a new welding robot in a new workshop, they can now produce large structures measuring up to three by six metres. [10.11.09] |
Short Read Assembly into Haplotypes
0.2 October 2008
ShoRAH is a software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.
ShoRAH is distributed under the GNU General Public License.
For changes between versions please see the file CHANGELOG.
ShoRAH has been tested under Linux and Mac OS X.
Please consult the INSTALL file for instructions.
It has ben reported that, on some architectures, the C++ code might fail to compile. Adding
#include <cstdlib> to both contain_src/contain.cc and freqEst_src/freqEst.cc at the top of the files should solve the issue (thanks for reporting this).
Line 193 of dec.py (del out_reads[mathc_rec.id]) should be commented out.
Next version of the software (summer 2009) will address these issues, and will contain several upgrades.
Niko Beerenwinkel
Nicholas Eriksson
Lukas Geyrhofer
Osvaldo Zagordi
The general inference procedure is described in:
The current implementation of the error correction step is not based on the k-means algorithm described in the PLoS paper. Rather, we use the Dirichlet process mixture for locally inferring haplotypes and correcting reads.
Wichtiger Hinweis:
Diese Website wird in älteren Versionen von Netscape ohne
graphische Elemente dargestellt. Die Funktionalität der
Website ist aber trotzdem gewährleistet. Wenn Sie diese
Website regelmässig benutzen, empfehlen wir Ihnen, auf
Ihrem Computer einen aktuellen Browser zu installieren. Weitere
Informationen finden Sie auf
folgender
Seite.
Important Note:
The content in this site is accessible to any browser or
Internet device, however, some graphics will display correctly
only in the newer versions of Netscape. To get the most out of
our site we suggest you upgrade to a newer browser.
More
information