Sentence examples similar to toolkit and aligned from inspiring English sources
Then reads with high sequencing quality and ranging from 18 30 nt in length were collected by Fastx-toolkit and aligned to Rfam database [ 54] and oyster mRNAs.
Raw reads were subjected to standard quality control procedures with the NGSQC-toolkit software and aligned to the human genome reference sequence (NCBI37/hg19) by the TopHat alignment software.
The coordinates of each BLASTN match were extracted using our customized Perl scripts, which utilized some modules of the BioPerl toolkit [ 85], and aligned with ClustalW [ 86] with default parameters.
The predicted genes of both genome sequences were compared using the local BlastN program in the NCBI toolkit and 1,590 aligned genes were used for the nucleotide substitution analysis by Nei's unweighted method I [ 33].
Raw reads were trimmed by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and aligned to B73 reference genome (AGPv2) using Tophat/Bowtie.
Briefly, raw reads were filtered using the NGS QC Toolkit (Patel and Jain 2012) and aligned against the reference genome using BWA (Li and Durbin 2009).
The HaplotypeCaller function [ 60] of the Genome Analysis Toolkit (GATK [ 38]) was used to identify variable sites between the amakihi genome and aligned honeycreeper reads using the MalformedReadFilter and default parameters.
Regions spanning the TSS from −200 to +100 positions were extracted and aligned to assess percent nucleotide composition at each position using the FASTX toolkit [ 58].
Reads were quality trimmed using the FASTX-Toolkit v0.0.13 and then aligned to the 1000 Genomes version of the human reference genome (human_g1k_v37) using the Burrows-Wheeler Aligner (BWA) v0.7.5a.
