Sentences with phrase «read alignment»

Heng Li's brilliant short read alignment tool finally went legit with a publication in Genome Research that came online this month.

Few short read aligners can handle the throughput of Illumina data and allow for gaps in read alignments, because speed and gapped alignment are at odds with one another.

Two papers by Langmead and team, Ultrafast and memory - efficient alignment of short DNA sequences to the human genome and Fast gapped - read alignment with Bowtie 2, have been cited in more than 12,000 scientific studies since 2009.

As a final step, one can use VarScan to limit variant calls to a set of targeted positions, which removes variants arising from spurious read alignments.

Given a file of read alignments, VarScan detects sequence variants, combines them by position and type, and then computes the read counts, average base quality, and number of strands supporting each allele.

If you're interested in reading more on ideas presented in the article below, I suggest reading Alignment Matters.

We have reviewed the research, and we have listened to members who are reading the alignment research — members who have asked us if we intend to go down the path indicated by the research.

This pipeline not only describes a set of sequential analytical steps, such as short reads alignment, genotype calling and functional variation annotation that can be conducted using open - source software tools, but also provides users a set of scripts to install the dependent software and resources and implement the pipeline on their data.

Heng's group soon developed a sequel to Maq, called BWA, that leverages this algorithm to speed up read alignments.

Also, we are continuing to evaluate other aligners, especially Bowtie, which offer comparable or even better speed at short read alignment.

Short read alignment.