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SV-STAT / Structural Variation detection by STAck and Tail

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Quantifies evidence for structural variation in genomic regions suspected of harboring rearrangements. SV-STAT extends existing methods by adjusting a chimeric read’s support of a structural variation by (i) the number of its soft-clipped bases and (ii) the quality of its alignment to the junction. SV-STAT is more accurate than alternative methods for determining base-pair resolved breakpoints. SV-STAT is a significant advance towards accurate detection and genotyping of genomic rearrangements from DNA sequencing data.

Nanopolish

Provides a nanopore consensus algorithm using a signal-level hidden Markov model (HMM). The main subprograms of Nanopolish are: (i) nanopolish extract which extracts reads in FASTA or FASTQ format from a directory of FAST5 files; (ii) nanopolish eventalign which aligns signal-level events to k-mers of a reference genome; (iii) nanopolish variants which detects single nucleotide polymorphisms (SNPs) and indels with respect to a reference genome; and (iv) nanopolish variants –consensus which calculates an improved consensus sequence for a draft genome assembly. Furthermore, Nanopolish contains an experimental option that will use event durations to improve the consensus accuracy around homopolymers.