mrFAST: Micro Read Fast Alignment Search Tool
...uding indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respec...eads, however it can return one "best" map location if the relevant parameter is invoked. More at ht...2974 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
...ftware is currently alpha level, feel free to use and report issues encountered. Canu is a hierachical assembly pipeline which runs in four steps: Detect overlaps in high...2957 days ago
MEDEA: Comparative Genomic Visualization with Adobe Flash
As the number of sequence and annotated genomes grows larger, the need to underst...mportant. Using the power of the human visual system to detect trends and spot ou...data sets. More at http://www.broadinstitute.org/annotation/medea/...2974 days ago
Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
Smash is a completely alignment-free method/tool to find...sualise genomic rearrangements. The detection is based on conditi...sing a FCM (Markov model), of high context order (typically 20). For v...gramoutput architecture, where the patterns are represented with sever...2974 days ago
RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
...he RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genome...dentifying genomic features (i.e., protein-encoding genes and RNA) and...RAST that is both customizable and extensible. In this paper, we desc...2973 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
...s enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even...2972 days ago
2960 days ago
2960 days ago
YASS :: genomic similarity search tool
...NA/RNA) sequences in fasta or plain text format (it produces local p...for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ....larity regions, and then tries to extend them to local alignments. T...overlapping seeds and a new hit criterion to ensure a good sensitiv...2968 days ago
Painless package development for R
...loping a package becomes so easy that it will be your default layout whenever you’re writing a significant amount of code. Before you get started be sure to check out: dev...2967 days ago