marbl/parsnp
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
C++NOASSERTION
Stargazers
- abyssloverAnyang, KR
- AdamtarantoThe University of Melbourne
- alienzjGPG
- audy@OneCodex
- bkilleRice University
- boulundKarolinska Institutet
- boydgreenfield
- cbertellLausanne University Hospital, Switzerland
- cfsancasFPS
- chrisgulvikUSA
- cmkobelNorges Miljø- & Biovitenskapelige Universitet (NMBU)
- Diamonds95
- druvusSweden
- ejuscamaytal
- erkiaunEstonia
- faithmanChengdu Research Base of Giant Panda Breeding
- fjell-dev
- flopezoQueen Mary University of London
- Fu-YileiBaylor College of Medicine
- Gab0Rio de Janeiro, Brazil
- gengce
- jrherrUniversity of Nebraska
- jrjhealey
- jrsistrAtlanta, Ga
- kokyriakidisUniversity of California, Santa Cruz
- liaochenlanruoPerfect
- mgalardiniTwincore & MHH
- NTNguyen13
- oschwengers@ag-computational-bio - JLU Giessen
- phraber
- sjackman@10xGenomics
- thanhleviet@quadram-institute-bioscience
- VeromanUSA
- wjideaCA
- yjx1217Sun Yat-sen University Cancer Center (SYSUCC)
- yujiehu0823