1978 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
...olicy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments. HECIL’s core algorithm by introducing an iterative l...1963 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
...(CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that cla...1960 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...rogram first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of...1951 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
...equences and in aligning next-generation sequencing reads/contigs against a reference coding sequence. For further details about the underlying algorithm see the original publication:...1915 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with simila...1915 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
...s of obtaining more robust STR genotypes. In particular, it accomplishes this by: Learning locus-specific PCR stutter models using an EM algorithm Mining candidate STR alleles...1898 days ago
1861 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
...vokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative function...1829 days ago
FLAS: fast and high throughput algorithm for PacBio long read self-correction.
FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy.1791 days ago