UnoSeq is a Java library to analyze next generation sequencing data (e.g. data generated by Illumina's mRNAseq method) and especially perform expression profiling in organisms where no well-annotated reference genome exists.
标签：RNA-Seq Alignment, De novo transcriptome assembly
Tool for predicting effects of variants for any genome in Ensembl. The web version is limited to 750 variants, but an API and Perl script are provided as well.
Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the dearth of efficient computational tools. Here, we present a new tool, VirusHunter, for th...
We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accuratel...
ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical pri...
ZORRO is an hybrid sequencing technology assembler. It takes to sets of pre-assembled contigs and merge them into a more contiguous and consistent assembly. The main caracteristic of Zorro is the treatment before and after assembly to avoid errors.
Screens through the genome in a recently mixed population such as African Americans, searching for segments with increased ancestry from one of the ancestral populations, which can indicate the position of disease genes
For viewing and analysing (eg with blast) DNA/protein sequences and feature tables. Start with command art . The Artemis Comparison Tool is started with act. Both require X-Windows.
A program, and associated scripts, to predict genes in eukaryotic genomic sequences.
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
Open Babel succeeds Babel: Program and library to interconvert between many file formats used in structural studies. Includes babel, obfit, obgrep and obrotate