What it does

This tool returns the results processed from either the S. aureus or R. sphaeroides set of short reads using ALLPATHS version 42807. These datasets can be viewed by using the Shared Data drop down menu and clicking Data Libraries.

The reason for the hard-coding of ALLPATHS to only display the results of these two bacterial datasets is to (try to) show a reproduction of the results from Table 2 reported in Luo et al., (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012, 1:18. These results produced by ALLPATHS involved using the Perl script PrepareAllPathsInputs.pl to initially transform the Fasta-formatted short read files into ALLPATHS input files before genome assembly.

The ALLPATHS software is developed by the Computational Research and Development group at the Broad Institute. Use of ALLPATHS should be accompanied with the following citation:

Ribeiro F, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, MacCallum I, Nusbaum C, Jaffe DB. Finished bacterial genomes from shotgun sequence data. Genome Research 22: 2270–7.

Outputs

Four outputs are generated by this tool:

1. Contigs
2. Scaffolds
3. in_groups - contains information on the nickname, library name and file names of the the data set used to execute the ALLPATHS process.
4. in_libs - describes and provides statistics of the files in the data set used in the ALLPATHS process.