The phrase "and realigned using the" is correct and usable in written English.
It can be used in contexts where something is being adjusted or modified with a specific method or tool.
Example: "The data was processed and realigned using the latest software to ensure accuracy."
Alternatives: "and adjusted with the" or "and modified through the".
Regions in the mapped dataset that would benefit from realignment due to small in/dels were identified using the GATK module RealignerTargetCreator, and realigned using the module IndelRealigner.
To minimize false positive SNP calls near insertion/deletion (indel) events, poorly aligning regions were identified and realigned using the GATK RealignerTargetCreator and IndelRealigner (GATK version 1.4-14 1.4-14ion 1.4-14]) (McKenna et al., 2010).
Sequences containing binding sites for human Sp1 (mostly footprints), were obtained from the TRANSFAC database (July 2007 release), mapped on the human genome, extracted with genome flanking sequences, and realigned using the SeSiMCMC Gibbs sampler [ 55] (see Additional file 6 for details).
Initial mapping results were transferred into indexed and sorted BAM format using SAMtools version 0.1.12a [ 24], and further recalibrated and locally realigned using the Genome Analysis Toolkit GATKK version 1.0.4905) software [ 25].
After this was accomplished, gaps were eliminated and sequences were realigned using the same algorithm and parameters.
The k 2, V A, and V RV images were realigned using the same transforms.
In the second experiment, the sequences with discrepancies were excluded from the benchmark test sets and each sequence set was realigned using the eight MSA programs.The quality of the resulting alignments was again measured using the CS score (Figure 5).
Proteins missing both individual domains were discarded and the clipped MSAs were realigned using the MAFFT [ 66] L-INSI algorithm.
The reads were realigned using the local realignment tool in Strand NGS.
The mapped reads were locally realigned using the genome mapping tool RealignerTargetCreator from the Genome Atlas Tool Kit (GATK) [ 15].
The SOLiD BAM files were locally realigned using the GATK local realignment utility [ 2].
