Rahul Nayak
A Bioinformatician
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X. Shirley Liu Lab
The research in our laboratories are focused on the following three areas: Bioinformatics Cancer Epigenetics More at http://liulab.dfci.harvard.edu/BEDOPS v2.4.26: high-performance genomic feature operations
By Jit 2855 days agogithub.com - BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2509 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2361 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...nQuire: A statistical framework for ploidy estimation using NGS short-read data
By Jit 2257 days agogithub.com - nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish...ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
By Neel 1907 days agogithub.com - ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1874 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...The "Ifs" and "Buts" of NGS Quality Control and Trimming
By BioStar 94 days agoNGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and...genomics public data links !
By Jit 1880 days agoconsole.cloud.google.com - List of publically available databases on google server. More at https://software.broadinstitute.org/gatk/download/bundle ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/. ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/
