Similar(60)
These aligners take advantage of the short read lengths for speeding up the alignment (by using hash tables for speeding up seed identification) which allows the processing of a larger number of reads in a reasonable time frame: Eland (Illumina): the mapping algorithm which is provided by Illumina as part of its analysis pipeline, divides each read into four parts (A, B, C and D).
However, as the number of substitution errors appears much more than the insertion/deletion errors, IDBA-Tran considers substitution error only for speeding up the alignment process.
Speeding up this flow matters.
We exploit this property to speed up the alignment process (Figure 6).
For all uniquely mappable reads, this tiered mapping approach can speed up the alignment to the human genome by 24 times on average.
MegaBLAST was developed to speed up the alignment for query sequences that are highly similar to the reference sequences and was used to align large-scale sequencing data.
Therefore, to speed up the alignment process we used NUCMER pipeline of MUMMER [ 34].
In addition, one may want to use automatically produced local alignments as anchor points to speed up the alignment procedure as outlined in [ 18].
By limiting the gapped alignment of the reads in the former subset to their associated chromosomes, the tiered mapping approach removes the unnecessary mapping attempts and thus speeds up the alignment step.
BLAST (http://blast.ncbi.nlm.nih.gov/) and FASTA (http://www.ebi.ac.uk/Tools/sss/fasta/) propose some restrictions to the sequence entries to speed up the alignment computation process, potentially at the cost of reducing quality.
Geographically, we are thousands of years overdue a shift in the planets alignments and I have this idea that nature allowed humans to be so dominant, only to help her speed up this change… so who else is looking forward to the new iPhone then?
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