ALLPATHS‐LG is a whole‐genome shotgun assembler that can generate high‐quality genome assemblies using short reads. It has been designed to use reads produced by new sequencing technology machines such as the Illumina Genome Analyzer. The current version has been optimized for, but not necessarily limited to, reads of length 100 bases. ALLPATHS is not designed to assemble Sanger or 454 FLX reads, or a mix of these with short reads.
ALLPATHS‐LG requires high sequence coverage of the genome in order to compensate for the shortness of the reads. The precise coverage required depends on the length and quality of the paired reads, but typically is of the order 100x or above. This is raw read coverage, before any error correction or filtering.
ALLPATHS‐LG requires a minimum of 2 paired‐end libraries – one short and one long. The short library average separation size must be slightly less than twice the read size, such that the reads from a pair will likely overlap – for example, for 100 base reads the insert size should be 180 bases. The distribution of sizes should be as small as possible, with a standard deviation of less than 20%. The long library insert size should be approximately 3000 bases long and can have a larger size distribution. Additional optional longer insert libraries can be used to help disambiguate larger repeat structures and may be generated at lower coverage.
Version on CSC's Servers
Taito: 51503 (default), 52488
To initialize the program you need to give command:
After this you can start using ALLPATHS-LG commands.
module load biokit
More information about ALLPATHS-LG can be found from: