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bioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...

sourceforge.net - AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET...

bitbucket.org - RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It...

kissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...

www.broadinstitute.org - The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete...

biobits.org - SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions    1.0: May 30, 2013: First public release on...

alignment: the mapping of a raw sequence read to a location within a reference genome. The mapping occurs because the sequences within the raw read match or align to sequences within the reference genome. Alignment information is stored in the SAM...

4dgenome.research.chop.edu - Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted...

abims.sb-roscoff.fr - Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common...

www.cbcb.umd.edu - VALET is a pipeline for performing de novo validation of metagenomic assemblies. VALET checks a number of properties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance from each other in the...