Sentence examples for alignment realignment from inspiring English sources

The exonic variant quality for the complete run is indistinguishable from a "standard" WGS analysis [see Additional files 2 and 3] but accomplished in only ~4 hours compared to the standard procedure of: alignment, realignment, recalibration; variant identification and recalibration; and variant annotation; which takes approximately 1 week.

There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences.

There is no need to reconstruct the genome space for any subsequent application, whereas in multiple alignment methods, realignment is needed for adding new sequences.

To improve this alignment, the realignment functionality provided by GATK [ 34] was applied prior to the SNV calling.

Following read alignment, local realignment was performed using GATK version 2.4 [ 8], and duplicates were then marked using Picard version 1.54 [ 9].

There is no need to reconstruct the genome space for any subsequent application, whereas in multiple alignment methods, realignment is needed for add-on new sequences.

Structural models were made using automated and manual modelling routines in an iterative manner using DeepView v3.7 SP5) [ 83, 84] for alignment and realignment of sequences and energy minimization of models and Swiss Model [ 84] software and servers for threading of models.

We applied the same filter thresholds as for the GATK dataset and used defaults settings otherwise (except for deactivating the base alignment quality realignment with the -B parameter: 'samtools mpileup -q 30 -Q 30 -B').

We used four methods to assess the degree of conservation for each sequence (Table 2): the original AVID-based alignments; local realignment using DIALIGN [ 18]; and 15-way PhastCons scores [ 19] obtained via the UCSC Genome Browser [ 20].

If the growth results in a mismatch of amino acid type or of alignment, then a realignment is attempted.

Results include the native FlowerPower subfamily-HMM based alignment and a realignment of the sequences using MUSCLE.