Error and Error Mitigation in Low-Coverage Genome Assemblies

Genome assembly quality: Assessment and improvement using the neutral indel model

(2010) S. Meader et al.   GENOME RESEARCH

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

The difficulty of avoiding false positives in genome scans for natural selection

(2009) S. Mallick et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

De novo fragment assembly with short mate-paired reads: Does the read length matter?

(2008) M. J. Chaisson et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH