Jit
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EAGLER: a scaffolding tool for long reads.
By Jit 2365 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2136 days ago Comments (1)bioinformaticsdotca.github.io - In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1351 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 2827 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...1mb long DNA with Nanopore technology
By Jit 2531 days agoLongest read of 1mb achievements with NanoporeCoverM: Read coverage calculator for metagenomics
By Neel 1304 days agogithub.com - CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. CoverM calculates coverage of genomes/MAGs coverm genome (help) or individual...PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 2299 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...URMAP, an ultra-fast read mapper
By Jit 1486 days ago Comments (1)github.com - URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves...List of popular bioinformatics software/tools
By Jitendra Narayan 4149 days ago Comments (28)samtools.sourceforge.net - In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.deepTools
By Martin Jones 3669 days agoUser-friendly tools for the normalization and visualization of deep-sequencing data
