Stroll Assembler 1.2.1

What is Stroll?

• STROLL is a fragment assembly program designed for large-scale (mega-base level) genome sequencing.

History

• Stroll was developed at the Brookhaven National Laboratory during the sequencing of the Borrelia Burgdogferi Bacterium. Stroll was designed for sequencing mega-base bacterial genomes like Borrelia. Stroll strategy is divided into two phases, first it does a thin coverage shotgun sequencing and later it closes the gaps by doing primer walking.

Algorithms and Data Structures used by STROLL

• Suffix array: Stroll uses a suffix array to quickly reject non-overlapping fragment pairs. This reduces the number of calls to the pair wise comparison.

• Fast banded pair wise comparison algorithm with affined penalties and base qualities: Stroll uses this algorithm to search for local similarities of two fragments.

• Overlap recovery strategy: Stroll uses the transitive relations to recover most of the undetected overlaps.

• Stroll also uses an incremental multiple alignment algorithm to add fragments into contigs one-by-one in the order of pair wise alignment quality.

System Requirements

•  Supported Operating Systems: Unix, Linux.

Downloads

•  Stroll Sources

• Computational Biology Project Report

Quick Installation Steps

1. Download the Stroll Sources

2. gunzip STROLL1.2.1.tar.gz

3. tar -xvf STROLL1.2.1.tar

4. cd STROLL1.2.1

5. make

6. now you can use stroll. read the README for more details.

this distribution was updated by johnny giusto <[email protected]>