Goldman Group - Software - SolidCaller

SolidCaller - Base Calling for SOLiD platform using alternative codes


SolidCaller is an independent implementation of trelis decoding of 2/4 base-encoding produced by the SOLiD™ platform when the Exact Call Chemistry module is used. The posterior decoding algorithm (MAP) to find the most probable base at each position is described in the Applied Biosystems white paper SOLiD™ System accuracy with the Exact Call Chemistry module .

SolidCaller supports various natural extensions of the algorithm described, including:

  • Viterbi decoding to find the most probable sequence of bases.
  • Decode into color-space rather than base-space.
  • Support for alternative ECC-style encodings.

SimSolid is a package for simulating reads from known (user-specified) fragments of sequence as if produced from the SOLiD™ platform with the Exact Call Chemistry module. The error profile used to generate the reads is empirically derived from analysis of a real machine run. SimSolid can also simulate reads using alternative ECC-style encodings.


SolidCaller and SimSolid are freely available under the GNU General Public Licence version 3 (see for further information). A copy of the licence is provided with the software.

SimSolid incorporates the optimised SFMT code for the Mersenne twister random number generator produced by Mutsuo Saito and Makoto Matsumotom, which is available from Hiroshima University under a three-clause BSD style licence.



Misc. routines for experimenting with alternative codes


8 November 2011
Initial release of code