Allpaths manual

 · ALLPATHS-LG is a short read assembler. It has been designed to use reads produced by new sequencing technology machines such as the Illumina Genome Analyzer. This version has been optimized for, but not necessarily limited to, reads of length bases.  · Plus, as suggested by the AllPaths-LG manual, if the pipeline needs to be re-run for any reason (whether it prematurely aborted or some of the input data or parameters were modified), Make will only run the commands it needs to. RPGC Manual Introduction Here we present a new approach for producing de novo whole genome sequences--recombi-nant population genome construction (RPGC)--that solves many of the problems encoun- We built a de novo genome assembly using ALLPATHS-LG (build ). We ˜rst prepared the data as ALLPATHS-LG suggests. Reads from two parents plus.

1. 1. 1. 1. Copy of Available bioinformatics software The following software packages are installed on the RCAC compute clusters. To access the software, use the module command as described in the RCAC user manual€. We then integrated the Newbler consensus shreds, Velvet consen-sus shreds, Allpaths consensus shreds, and a subset of the longinsert read pairs using parallel Phrap (High Performance Software, LLC). Possible misassemblies were corrected, and some gap closure was accomplished with manual editing in Consed ().Automatic annotation for each. A more detailed discussion of each of these directories, as well as a list of other command-line arguments, is avaible in the user manual. Other ALLPATHS-LG utilities may be found in the directory /soft/allpathslg/VER/bin. where VER is the version of ALLPATHS-LG you are using.

MASS - Multiple Assembly Creation. This tool enables the user to try different assemblers with different settings. Currently, the following assemblers are supported by RAMPART (brackets below indicate tool name to use if config file - case insensitive): Abyss V (ABYSS_V) ALLPATHS-LG V50xxx (ALLPATHSLG_V50). Defaults to all vertices. Character constant, gives whether the shortest paths to or from the given vertices should be calculated for directed graphs. If out then the shortest paths from the vertex, if in then to it will be considered. If all, the default, then the corresponding undirected graph will be used, ie. not directed paths are searched. The latest version of ALLPATHS-LG, including the manual and example data, is available for download via our ftp site, and is released under this license. Note that as of release , GCC (or higher) is required. If you are unable to meet this new requirement then please download the last pre release.