Computer simulation of genetic mechanism !!
...istasis, linkage disequilibrium patterns and haplotype blocks for genome-wide intera...apSim A simulation tool for generating haplotype data with pre-specified allel...imPed A Simulation Program to Generate Haplotype and Genotype Data for Pedigre...2969 days ago
Tools and Method for Haplotype phasing !
...ned in these results, however, is best exploited through phased haplotypes, which classify the alleles...es not specifically observe which of the two parental chromosomes, or haplotypes, falls on a specific allele....1333 days ago
InfoGenomeR: Integrative reconstruction of cancer genome karyotypes
...ectivity among genomic segments at the genome-wide scale. InfoGenomeR integrates cancer purity and ploidy, total CNAs, allele-specific CNAs, and haplotype information to identify the o...1090 days ago
2741 days ago
Genome Assembly Tools and Software - PART2 !!
...cle-Basis Algorithm for Accurate Haplotype AssemblyHapCompass for p...COMPASS will assemble reads into haplotypes. GAM-NGS 1.1b – Genom...ndash; Short Reads Assembly into HaplotypesShoRAH is a software pac...and SOLiD. hapAssembly – Haplotype Assembly from Whole-Genome Se...2680 days ago
Bioinformatics in Africa: Part7 - Tunisia
...;signal transduction pathways and statistical analysis of human sequence variation data (haplotype reconstruction and...1177 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
...s_software/hapgen/hapgen2.htmlHapSim A simulation tool for generating haplotype data with pre-specified allel...http://www2.unil.ch/popgen/softwares/quantinemo/RECOAL Simulates new haplotype data from a reference populat...3731 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...opulation; Fairly popular Input: Reference Haplotypes: Links to 1000 Genomes and H..., MNPs; reports variants based on alignment; haplotype based Input: BAM- uses BAMto...k, Pathway Association Analysis, Genome-wide Haplotype Analysis, Input: PLINK input...2903 days ago
Phased Human Genome Assembly !
...;System. Using the FALCON-Unzip assembler, maternal and paternal haplotypes were resolved over more than 80% of the genome. Maternal and paternal haplotype blocks were then further phas...2030 days ago
Bash script to simulate a genome !
...grep -v "^#"|wc -l # 2830139 # ~2% het rate # get only 1 haplotype from the "diploid" reference...bgzip -@75 \ > GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.haplotype0.fasta.gz # make ref...912 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccura...Tags: HapCUT2, robust, accurate, haplotype, assembly, diverse, sequencing, technologies
2176 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to imp...Tags: Ranbow, haplotype, assembler, polyploid, genomes, Assembly, NGS
2159 days ago