2308 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method...cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non recombining part of sex chromosomes). How does SEX-DETec...individuals need to be genotyped; SEX-DETector takes files produced by Rea...2177 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genom...atwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo...2194 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vit...mentary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assembli...2194 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
Provides interactive, configurable and...gant graphics visualization of the chromosomes or chromosome regions of any living organis...nts (like genes, SNPs etc.) on the chromosome plot. It introduces a special...es like visualizing multiple sets, chromosome heat-maps, group annotations,...1861 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral geno...alidate the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and th...2186 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implem...ppy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.26...2162 days ago
Indexcov: fast coverage quality control for whole-genome sequencing
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant c...-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a s...2086 days ago
1961 days ago
EyeChrom: Visualizing Chromosome Count Data From Plants
It's goal is to show chromosmal data per genus. Select the genus, and the plot will show the records found for it in the Chromosome Counts Database. note: Report...1954 days ago