:: DESCRIPTION
fqCleanER is a command line tool to ease the different standard preprocessing steps of short high-throughput sequencing (HTS) reads.
::DEVELOPER
Alexis Criscuolo (alexis.criscuolo@pasteur.fr)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
VIPER (Visual Pedigree Explorer) combines an improved ResSpecies algorithm for genotype inheritance checking and inference with a novel space-efficient visualisation of pedigree structure in a desktop tool for exploring then cleaning data errors in pedigree/genotype datasets.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012;13 Suppl 8:S5. doi: 10.1186/1471-2105-13-S8-S5. Epub 2012 May 18.
VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.
Paterson T, Graham M, Kennedy J, Law A.
:: DESCRIPTION
SeqyClean is a Software Tool for Comprehensive Preprocessing of Sequence Data.
::DEVELOPER
Institute for Bioinformatics and Evolutionary Studies
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Overly imprecise or erroneous geo-references are a major issues when using species distribution data from large databases compiled from various sources, such as public data aggregators (e.g. GBIF).
CoordinateCleaner automatically cleans databases from records with potentially erroneous coordinates. It accounts for errors most commonly found in biological collections, for instance invalid coordinates, coordinates in the sea, coordinates assigned to country centroids, capitals or biodiversity institutions.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zizka A, Silvestro D, Andermann T, Azevedo J, Duarte Ritter C, Edler D, Farooq H, Herdean A, Ariza M, Scharn R, Svanteson S, Wengtrom N, Zizka V & Antonelli A
CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases.(in press)
Methods in Ecology and Evolution, 0:0-0, doi:10.1111/2041-210X.13152,
:: DESCRIPTION
RC454 (ReadClean454) is a program that takes a set of 454 read and quality files as well as a consensus assembly for those reads and corrects for known 454 error modes such as homopolymer indels and carry forward/incomplete extension (CAFIE).It will also correct for any indel that breaks the reading frame, unless it occurs in more than 25% of the reads.
::DEVELOPER
Computational R&D, The Broad Institute, Cambridge, MA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
