The phrase "alignment the reference" is not correct in written English.
It seems to be missing a preposition or article to make sense in context.
Example: "We need to ensure the alignment of the reference before proceeding with the project."
Alternatives: "alignment of the reference" or "aligning the reference".
All placement accuracy statistics for EPA and Phyclass were calculated by first deleting from the tree and the reference sequence alignment the reference sequence from which the query was extracted.
To optimize the alignment, the reference plastome was chosen for each evolutionary lineage (Amborella trichopoda for basal angiosperms, Liriodendron tulipifera for magnoliids, Nandina domestica for basal eudicots, Arabidopsis thaliana for rosids, Nicotiana tabacum for asterids, and Acorus calamus for monocots), and all sequences from representatives of this group were aligned against it.
All datasets exhibited a good read quality (Phred score > 20) and a high fraction of read alignment to the reference genome (alignment score ≥ 93%) using HISAT.
The second letter, 'm/u/N', indicates the alignment to the reference genome sequence, 'm' represents multiple alignments, 'u' represents unique alignment and 'N' represents no alignment results.
This was converted into a wallaby- and a human-referenced alignment by removing columns from the multiple alignment, where the reference sequence contained gaps.
Alignment to the reference was done using bowtie2 2.1.0 in local alignment mode.
This function prints a coloured RC-MSA representation of the sections of the alignment in which the reference alignment and the alignment to be inspected differ.
First, reads were required to have a best alignment to the reference assembly with at least 3% more identical nucleotides than the second-best alignment.
This methodology consists of: comparing a shape fingerprint; locating common reference shapes; and then reuse of the alignment to the common reference, where the shape overlap and the feature overlap are computed at that recycled alignment to the reference shape.
For each alignment against the reference, the genomic position and orientation was extracted.
