ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82224 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...mplementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that...2216 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact w...2182 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...s that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32...2213 days ago
LAMSA: fast split read alignment with long approximate matches
...ts. The alignments of the fragments are then used for implementing a sparse dynamic programming (SDP)-based split alignment approach to handle the large or non-co-linear variants....2209 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, e...2201 days ago
2196 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands...ng the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing e...2164 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...nbsp;BLAST-based ANI solver and it achieves two to three orders of magnitude speedup. Therefore, it is useful for pairwise ANI computation of large number of genome pairs. More...2150 days ago
Indexcov: fast coverage quality control for whole-genome sequencing
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize...2103 days ago