Sentence examples for a merged alignment from inspiring English sources

From a merged alignment that contained Illumina reads from both genotypes (hereafter referred as IL assembly) we separately called SNPs for each read group in positions where there was read depth of at least 6, applying a base quality threshold of 20.

Relative rate tests were performed on a single merged alignment and on each of the 84 multiple alignments using Tajima's method [ 44, 45].

Finally, we aligned the merged alignment with the unaligned 24 sequences.

When we perform further hand-curation of hypervariable regions of the 16S V3 in the merged alignment

Variant calls from this merged alignment were performed in two subsequent steps: (1) A global variant call (i.e. including both read types at each variants position) was conducted using the SAMtools mpileup command.

An example of the merged alignment in which the hypervariable region was further hand-curated is given in Figure S2d.

The merged alignment was then exported both as consensus fasta sequences as well as a BAM file for use in subsequent analyses.

Although the difference was relatively small (6%), it was significant by the χ2 test (P <0.0001) when the merged alignment was tested.

Then, the consensus sequences of black grouse were extracted from the merged alignment file by the 'samtools mpileup', 'bcftools' and 'vcfutils.pl' (vcf2fq) pipelines from the SAMtools suite.

Amino acid alignment using MAFFT (Katoh and Standley 2013) of 75 single-copy orthologs with less than 10% alignment gaps were concatenated, and the distance matrix of the merged alignment was calculated using ProtTest (Abascal et al. 2005).

For the 500 bp PET libraries sequenced on the HiSeq 2000, we aligned each lane of data in parallel, merged alignments into a single file and inferred fragment size distributions using tools within the ABySS package.