Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences.
Since the results showed that the behaviors of the three mappers were complementary to each other, we sought to integrate the characteristics of the mappers by scoring them to gain robustness against artifacts (e.g. sequencing errors and aligning errors).
We evaluated three major areas of possible errors in aligning IMS channels and the NTP-independent private sector.
We evaluated DNA quality with the metrics: percent of the clusters that pass quality filtering, number of sequences that align to the phiX174 reference genome, and the overall percent error rate for those aligning phiX174 sequences.
Although all the sequences we obtained from NCBI were comparable in size to the human sequence, we cannot exclude annotation errors and, therefore, aligning of paralogous domains.
Increasing allowed alignment mismatches helps overcome missing genotypes, inaccuracies in the reference genome, and errors in the sequence reads, but also results in increased erroneous sequence alignment, particularly when aligning shorter reads.
We considered whether the dramatic increase in indel rates we observed in disordered regions could cause the difficulty in aligning disordered regions, and speculated that errors in alignment could explain the rapid rates of substitutions observed in disordered regions over long evolutionary distances.
On the subject of aligning coding DNA in presence of frameshift errors, some related ideas were presented in [ 22, 23].
During the assembly process, sequencing errors can be fixed by aligning different traces, but the software can also reduce polymorphisms and misplace those trace sequences because of the repeats.
We showed that the BWA-SW program used by DeconSeq has a high sensitivity (including repetitive regions) for sequences with low error rates or longer reads when aligning human DNA to the reference genome.
Thus, it may also be worth considering positions where both the C-90 and the C-100 set of reads display a V-shape, or one may consider a more tolerant error limit for the not perfectly aligning set (in particular, allowing short gaps).
