Jit
Enthusiast computational biologist with business dream !!!
Our Sponsors
Related items
QuorUM: An Error Corrector for Illumina Reads
By BioStar 1752 days agowww.genome.umd.edu - We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 2725 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2374 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...nanofilt: Filtering and trimming of long read sequencing data
By Jit 2307 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2133 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 1349 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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2393 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1760 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...CovCal: Coverage / Read Count Calculator
By Jit 3081 days ago Comments (1)apps.bioconnector.virginia.edu - Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/configuration and genome size, then select what you want to calculate. Written by Stephen...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 2552 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...
