Sentence examples for many alignment tools from inspiring English sources

Since the alignment process is computationally intensive, many alignment tools are designed as parallel applications, typically targeting multicore platforms.

For many alignment tools these effects become more pronounced when additional sequences are added to the analysis.

To keep pace with developing NGS technologies, many alignment tools have been developed for both short and long reads.

As the mapping of a read to a location in the reference genome may not be accurate, many alignment tools report a mapping quality score as an indicator of the likelihood that the mapping is accurate.

Alignment: while many alignment tools perform well and with high sensitivity (Homer et al., 2009; Li et al., 2008; Ning et al., 2001), the fast increase of generated read volumes has led to algorithms exploiting the Burrows–Wheeler transform, reducing runtime by two orders of magnitude and thus facilitating alignment of very deep read sets (e.g. Li and Durbin, 2009; Li et al., 2009).

We have experimented with many different alignment tools and consistently found the same problems in our eQTL mapping.

Many standard alignment tools and pipelines, such as Bowtie, BWA, TopHat and GATK [ 39, 40, 48, 49] have been established with vast successes in general analysis of genome-wide sequencing data.

Since many EST alignment tools (such as blat [ 21]) take advantage of splice site consensus sequences to maximize speed and accuracy, some introns that deviate from the expected patterns might be missed.

The size of the deletions covered by the split-reads can range up to tens of thousands of bases, and this makes BLAT well suited for mapping such reads back to the genome, since it not only allows small gaps and mismatches within the alignment like many other alignment tools, but also takes into account large gaps due to its initial purpose to handle introns in RNA/DNA alignments [ 27].

NGS has led to a huge amount of sequencing data which has rendered many existing sequence alignment tools obsolete.

Currently, many RNA-Seq alignment tools, including GSNAP [ 15], OSA [ 16], STAR [ 17], MapSplice[ 18], and TopHat [ 19], use reference transcriptomes to inform the alignments of junction reads.