Function
WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaf...
Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are desig...
CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36)&nb...
Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly progr...
OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file for...
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 SNP...
Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous seq...
A probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Str...
In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan...
gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb...