ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for solexa reads (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.
1. Does not require the user to copy fastq input files from the source directory like solexa_public.
2. Does not require the user to copy the wrapper script to another directory. You can call it from the original destination by giving a full path to where the script lives.
3. Requires a config file which outlines all the parameters like input file, input directory, output directory, seed length etc.
4. User can submit multiple alignments to the cluster with different parameters.
Allows users to run the alignments for the whole genome using ELAND. The program uses the seed length to find all the possible matches for a particular read and then extends the seed upto the read length, scoring each position based on the quality scores, and picks the best possible alignment. In addition, it generates QC reports and other formats as soon as the alignment is finished.