Sentence examples for low coverage depth from inspiring English sources
While Y sequences often do have low coverage depth, it is often not sufficient to classify a sequence as Y-linked solely by low coverage depth.
But in a low coverage depth situation, the performances of SWA are a little down.
So the appropriate sliding window can improve the performances of SWA and compensate the read loss of low coverage depth.
The coverage depth distribution shows that the fraction of uncovered bases at low coverage depth increased dramatically in all samples that had undergone WGA.
Although most of these tumors were sequenced at low coverage depth, we identified 2183 and 3138 mutated genes from respectively the CRC and EM tumor data sets.
Using a large k-mer has the advantage of resolving more repeat regions; whereas, use of small k-mers is advantageous for assembling low coverage depth and removing sequencing errors.
Nonetheless, it is clear that under some circumstances variant calling is significantly impacted by post-mortem damage patterns and low DNA availability typical of aDNA samples, particularly so for accuracy in SNP calls at high levels of damage, and for overall indel and SNP recovery at low coverage depths.
Since in general the cost of correcting the reads in terms of running time and memory usage is significant, in the following we present the results obtained using the set of long reads non-corrected LR-E with the lowest coverage depth, x20.
Due to likelihood of the misassembly of contigs with low coverage and depth, we remapped the reads to the assembled transcripts using Bowtie2 [ 61] and SAMtools [ 62] and removed those contigs with less than 75%% of sites with at least 2× from the datasets.
All SNPs for which the second allele in the same sample was not identified by 454 sequencing were among SNPs with the lowest read coverage depth.
Indeed, all the minor SNP alleles not identified by 454 sequencing were among those with the lowest read coverage depth (~3-5× per sample, see Additional file 5, Table S2).
