[PMID: 29182778] [Nucleic Acids Research]
Jointly aligning a group of DNA reads improves accuracy of identifying large deletions
“a method to jointly align reads to a genome, whereby alignment ambiguity of one read can be disambiguated by other reads. We show this leads to a significant improvement in the accuracy of identifying large deletions (≥20 bases)”
[PMID: 29304372] [American Journal of Human Genetics]
A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data
“Here, we used several datasets to empirically develop a detailed workflow for identifying germline CNVs >1 kb from short-read WGS data using read depth-based algorithms.”
[PMID: 28974235] [Genome Biology]
Alignment-free sequence comparison: benefits, applications, and tools
A review of Alignment-free sequence analyses tools.
[PMID: 28945707] [Nature Methods]
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
“a tool that combines fast mapping, error correction, and de novo assemblyfor processing single-molecule sequencing reads”
[PMID: 28522612] [Genome Research]
GenomeVIP: a cloud platform for genomic variant discovery and interpretation
“an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure.” Work from Li Ding.
[PMID:28436466] [Nature Methods]
Genome-wide profiling of heritable and de novo STR variations
“a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations.” Work from Yaniv Erlich.