The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.
Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for explor...
Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to ...
CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.
We propose a novel way of analyzing reads that integrates genomic locations and local coverage, and delivers all above mentioned predictions in a singl...
标签：Mapping, RNA Seq analysis,RNA-Seq Alignment, Alternative Splicing, Fusion genes, Fusion transcripts, SNP discovery,InDel discovery
Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
Curtain is a Java wrapper around next-generation assemblers such as Velvet which allows the incremental introduction of read-pair information into the assembly process. This enables the assembly of larger genomes than would otherwise be possible within existing memory constraints.
remove adapter sequences from high-throughput sequencing data using alignment
cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example whe...
discoSnps : qualitative de-novo SNP caller. Extremely low memory and time efficient. No reference genome needed. Call both homozygous and heterozygous SNPs.
标签：Population Genomics,Comparative genomics,Barcoding, DNA-Seq, De novo assembly, Genotyping, High-throughput sequencing
Tool for manual and automatic sequence assembly, analysis, editing, sample processing, metadata integration, file format conversion and mutation detection.
EBCall is a software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate m...
Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.