The software scans the reading frames of all gene sequence files and counts conserved and nonconserved nucleotide sites.
The cleanadaptors program scans the reads, identifying sections, which show 85% or higher matching with any of a series of adaptor sequences (the threshold is adjustable) in the sequenced reads and then the program removes the adaptor sequences from the sequenced reads.
Once a set of corrections has been determined for a read, Rcorrector scans the read and selectively refines those at nearby positions.
As shown in Figure 6a, when Max _ D_ Sizeis smaller than 1 k, the most time-consuming step is loading the reference sequence and scanning the read file.
At run time, Rcorrector scans the read sequence and, at each position, decides whether the next k-mer and each of its alternatives are solid and therefore represent valid continuations of the path.
To find a start node in the graph from which to search for a valid path, Rcorrector scans the read to identify a stretch of two or more consecutive solid k-mers, and marks these bases as solid.
Hapler scans the reads first in order of first covered SNP position and secondly by length; for each such read R, those reads R r which are made redundant by R are subsumed, or "masked" by R. R r is then removed from consideration as a masking read itself.
In order to reduce memory requirement, each time Pindel loads one chromosome into memory and scan the entire read alignment file, examining reads associated with the current chromosome.
The first level is a hash table to store all the locations of heterozygous SNPs from a given individual, and we therefore scan all the reads from the alignment file to identify the relevant ones.
But one teacher recalls coming back to a room after school to pick up forgotten supplies and seeing young McNair inside, scanning the board, reading the news.
