Jit
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ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 3017 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 2278 days agogithub.com - ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 384 days agogithub.com - HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a...Bioinformatics approach to Boar Taint
By Rahul Agarwal 4832 days ago Comments (3)Meat products obtained from intact male pigs often produce offensive smell or odour which is recognized as a complex genetic trait called boar taint.Androstenone and Skatole in the fat primarily cause boar taint. Metabolism of androstenone and...A-allele of SLC24A5 gene is found to be responsible for variation in skin color of South-East...
By Rahul Agarwal 4714 days agoMore is the A -allele, More is fairer the Skin !!SNPGenie
By Jit 3480 days agogithub.com - SNPGenie is a Perl script for estimating evolutionary parameters, mainly from pooled next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data. SNP reports (acceptable in a variety of formats) much each correspond to a...RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS...
By Surabhi Chaudhary 2415 days agogithub.com - RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows. Single-SNP GWAS with RGWAS.normal function SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests...DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 2033 days ago Comments (1)github.com - DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools...maftools
By Surabhi Chaudhary 1757 days agogithub.com - With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Genome Atlas Project has sequenced over 30 different cancers with sample size of each cancer type...SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 2483 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...
