PEWO: a collection of workflows to benchmark phylogenetic placement
Benjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric Rivals
Bioinformatics, btaa657, https://doi.org/10.1093/bioinformatics/btaa657 2020
Free author version https://hal.archives-ouvertes.fr/hal-02905244
Sherpas is a new NGS tool capable of predicting recombination in viral read sequences, given a tree and reference sequences of known virus groups.
See preprint on bioRxiv (Posted June 22, 2020):
Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
10.1101/2020.06.22.161422
Background. Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig describes the …
Philippe et al. (2011) proposed a data structure called Gk arrays for indexing and querying large collections of high-throughput sequencing data in main-memory. The data structure supports versatile queries for counting, locating, and analysing the …