A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.
标签：Sequence analysis, DNA-Seq,Alignment, De novo sequencing,Exome analysis, Exome and whole genome variant detection, Genetics, Whole Genome Resequencing, Next Generation Sequencing,Genomics
Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples.
标签：Next Generation Sequencing,Cancer biology, Genomics, Copy number estimation
TMAP is a short read aligner specifically tuned for data from the Ion Torrent PGM
TMAP is a short read aligner specifically tuned for data from the Ion Torrent PGM
The ChIP-Seq web server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. It is an open system designed to allow interopera...
"BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to f...
Strand NGS formerly Avadis NGS is a desktop software platform for alignment, analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms. It supports workflows for RNA-Seq, DNA-Seq, small RNA-Seq, ChIP-Seq, and Methyl-Seq data analysis. Strand...
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.
标签：Resequencing, Alignment,Quality Control, RNA-Seq Alignment, Alternative Splicing, Whole Genome Resequencing, SNP discovery,Phylogenetics, Metagenomics,Read Binning
CoNAn-SNV is a probabilistic framework for the discovery of single nucleotide variants in WGSS data. This software explicitly integrates information about copy number state of different genomic segments into the inference of single nucleotide variants.
PeakTrace is an alternative basecaller for improving the quality and read length of Sanger DNA sequencing traces. The PeakTrace basecaller works with trace files produced by the ABI 310, 3700, 3100, 3130, 3730, and 3500 DNA sequencers. MegBACE sequencers are also supported.
kisSnp compares two sets of NGS raw reads, detecting Single Nucleotide Polymorphism occurring between the two sets. The two sets typically come from the sequencing of two individuals from the same species or from closely related species.
标签：Comparative genomics,Comparative transcriptomics,Gene annotation retrieval, SNP discovery, InDel discovery
Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.
标签：Small RNA Sequencing, RNA-Seq,Whole Genome Resequencing, De novo Sequencing
Rsubread is Bioconductor R package, which provides facilities to performing read alignments using the Subread aligner. It also includes other functionalities such as featureCounts read summarization function.