We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content.
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.
Utility for working on BAM files analogous to samtools (see below) thus avoiding need to store and work on larger text SAM files where possible.
C++ API & command-line toolkit for wo...
Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and meth...
标签：Genomics, Sequencing, DNA methylation, Epigenomics
A probabilistic framework is described to predict the alignment to the genome of all paired-end read transcript fragments in a paired-end read dataset. Starting from possible exonic and spliced alignments of all end reads, our method constructs potential splicing paths connecting paired...
BiQ Analyzer HT is an enhanced version of BiQ Analyzer that provides extensive support for high-throughput bisulfite sequencing. BiQ Analyzer HT facilitates the processing, quality control and initial analysis of single-basepair resolution DNA methylation data. It was developed for deep...
标签：Epigenomics, DNA methylation,Bisulfite Sequencing
Genotype-calling algorithm that estimates parameters underlying the posterior probabilities in an adaptive way rather than arbitrarily specifying them a priori. The algorithm applies the well-known EM algorithm to an appropriate likelihood for a sample of unrelated individuals with next...
The VariantClassifier is a software tool for hierarchically classifying variants based on the genome annotation that is provided. Instead of looking at a region of the genome and seeing all the features relative to each other on the genomic axis, the VariantClassifier inverts the proces...
A scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly.
Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data. SNPs may be called using the Atlas-SNP2 application and indels may be called usin...
DeconSeq can be used to automatically detect and efficiently remove any type of sequence contamination from metagenomic datasets, including human or other host sequences. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read lengt...