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The spike-in can be done at low levels that would nonetheless generate a large enough number of reads to enable identification of minor contaminants.
It is likely that sequencing assays artificially introduced more calls for C bases in the sequence reads to enable the alignment of those sequences to the expected target, such as new exon-exon junction or a genomic insertion/deletion.
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Each study was read and re-read to enable the reviewer to familiarise themselves with the study findings and the methods used.
RAD-Seq is typically applied to multiplexed samples, where DNA fragments are ligated to a sample-specific barcode sequence for pooled sequencing, with subsequent in silico assignment of reads to samples enabling individual and population-level genotyping [ 13, 14].
The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels.
The 454 Titanium sequencing platform offers an ideal combination of throughput and long read length to enable de novo sequence assembly of whole genomes.
Check the "Mark as read" box to enable this.
Alignment of the paired-end reads to the reference genome enables identification of putative genomic rearrangements.
However, the presence of a reference sequence enables reads to be aligned to the reference which is much faster and allows for lower sequence depths than de novo assembly [ 17, 18].
As short insertions are likely to be fully contained in several reads, mapping donor reads to a reference genome enables simultaneous discovery of the sites and contents of insertions (Albers et al., 2011; DePristo et al., 2011; Li et al., 2009; Ye et al., 2009).
Reads sampled from different genomic locations may be misplaced in the same contig either due to hash collisions (contig construction stage) that enable dissimilar reads to share the same min hash value; or because of the graph partitioning strategy (contig clustering stage) employed to merge contigs via common reads.
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