:: DESCRIPTION
FLAM-seq is a rapid and simple method for high-quality sequencing of entire mRNAs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Legnini I, Alles J, Karaiskos N, Ayoub S, Rajewsky N.
FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.
Nat Methods. 2019 Sep;16(9):879-886. doi: 10.1038/s41592-019-0503-y. Epub 2019 Aug 5. PMID: 31384046.
:: DESCRIPTION
FunctionSIM is a bioinformatics tool to generate microbial DNA sequences. As standalone software it allows users to simulate metagenomic sequence datasets that can be used as standardized test data for planning metagenomic projects or for benchmarking software in functional metagenomic analysis.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ArrayMaker is a user-friendly tool which extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
Willet CE, Haase B, Charleston MA, Wade CM.
Bioinformatics. 2014 Oct 21. pii: btu691.
:: DESCRIPTION
GenoMS is a tool for sequencing a small set of proteins using an imperfect database and tandem mass spectra. The database need not contain full protein sequence, but instead can contain exons or partial sequences. The database can also be a small region of the genome. Tandem mass spectra should be from overlapping peptides produced from digestion by multiple proteases.
::DEVELOPER
Natalie Castellana ,CCMS The Center for Computational Mass Spectrometry
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Template Proteogenomics: sequencing whole proteins using an imperfect database.
NE Castellana, V Pham, D Arnott, JR Lill, V Bafna. (2010).
Mol. Cell. Proteomics, 9, 6:1260-70.
:: DESCRIPTION
QPLOT calculates various summary statistics some of which are plotted in a PDF file. These statistics can be used to assess the sequencing quality of sequence reads and include empirical base quality scores, GC biases, insert size distribution, depth distribution, genome coverage, empirical Q20 count, and so on.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis,
“QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,”
BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181
:: DESCRIPTION
Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals, but can also process single genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA
Large multiallelic copy number variations in humans
Nature Genetics (2015) doi:10.1038/ng.3200
Handsaker RE, Korn JM, Nemesh J, McCarroll SA
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Nature genetics 43, 269-276 (2011)
:: DESCRIPTION
BStools is a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites.
::DEVELOPER
:: SCREENSHOTS
N/a
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.
Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J.
Bioinformatics. 2015 Feb 13. pii: btv089
:: DESCRIPTION
AKSmooth is a statistical method that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Bioinform Comput Biol. 2014 Dec;12(6):1442005. doi: 10.1142/S0219720014420050.
AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.
Chen J1, Lutsik P, Akulenko R, Walter J, Helms V.
:: DESCRIPTION
SCORE-Seq is a command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. A detailed description of the methods is given in Lin and Tang (2011). The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lin, D. Y. and Tang, Z. Z. (2011).
A General Framework for Detecting Disease Associations With Rare Variants in Sequencing Studies.
American Journal of Human Genetics, 89, 354-367.
:: DESCRIPTION
Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait.
Stacks: building and genotyping loci de novo from short-read sequences.
G3: Genes, Genomes, Genetics, 1:171-182, 2011
