Compared with a state-of-the-art aligner, SALT has a similar speed but higher accuracy. SALT uses 5.8 GB of RAM to index a human reference genome (GRCh38) and incorporates 12.8M UCSC common SNPs. The SNP-aware alignment tool (SALT) is a fast, memory-efficient, and SNP-aware short read alignment tool. By contrast, considering only single nucleotide polymorphism (SNP) information will reduce the complexity of the index and improve the speed of sequence alignment. Aligning reads to a graph-model-based index that includes all types of variants is ultimately an NP-hard problem in theory. However, compared to linear reference aligners, an aligner that can store and index all genetic variants has a high cost in memory (RAM) space and leads to extremely long run time. Recently, a number of aligners have begun to map reads to populations of genomes, which can be represented by a reference genome and a large number of genetic variants. This limitation can introduce bias and impact the sensitivity and accuracy of mapping. However, such a linear reference genome represents the genome of only one or a few individuals and thus lacks information on variations in the population. Conventional DNA read aligners map reads to a linear reference genome (such as the GRCh38 primary assembly). The accuracy of sequence alignments directly affects the accuracy of downstream analyses, such as variant calling and quantitative analysis of transcriptome therefore, rapidly and accurately mapping reads to a reference genome is a significant topic in bioinformatics. DNA sequence alignment is a common first step in most applications of high-throughput sequencing technologies.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |