Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...lgorithm learns a posterior transition/emission probability distribution for each long read and uses this to correct errors in these reads. Using datasets from two DNA-seq BAC clones (...2082 days ago
2052 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
...o each other, in the same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm that identifies CSBs in large genomic datasets. The discovered CSBs are rank...2017 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
...al kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand...2017 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
...ap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standard file formats. Bui...1996 days ago
BLAST options, setting and defaults
...her sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or&...1970 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
...bsp;of SiLiX, based on MPI, is also available in this package and has been proved to be scalable, so that its allows the study of very large datasets. SiLiX is already included i...1968 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
...s hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with...1945 days ago
Roary: the Pan Genome Pipeline
...notated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, so...1928 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
...llowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional seq...1901 days ago