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, all...
Genome STRiP (Genome STRucture In Populations) is a suite...using data from multiple individuals.Genome STRiP looks both across and within a set of sequenced genomes to detect variation. The met...ts, but the method gains power across genomes and processing more genomes...
...sMap is a program for convenient conversion of genome coordinates (or annotation fi...FF/GTF, VCF.
CrossMap is designed to liftover genome coordinates between assemblie...;a program for aligning sequences to reference genome.
We do not recomme...
...lar, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the...
OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBan...or the creation of high-quality, detailed circular maps of organellar genomes like the plastid genome (plastome) or the mitochondri...
...ftware that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcr...choice of the post-treatment depends on the availability of a reference genome/transcriptome and on the need...
...ress has greatly facilitated de novo genome sequencing. However, de...isualization and quality assessment of de novo genome assemblies
Citation
This so...isualization and quality assessment of de novo genome assemblies.
In brief, our sc...
...iscovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6): R84. doi...
...ifferent gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE wi...s will lead to wrong prediction of initial exons in most cases.
http://genome.crg.es/courses/Bioinformatics...
gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and...tes (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or...et. It is especially useful for newly sequenced genomes that have not been well anno...