Neel
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Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 1606 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...
Genome Browsers
Last updated 4116 days ago by Rahul Agarwal Comments (2)Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc. Following are the weblink for different available...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. ...ACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 2543 days agowww.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...WhatsHap: fast and accurate read-based phasing
By Jit 2370 days agowhatshap.readthedocs.io - WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Features Very accurate...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1966 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 1752 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
By Jit 1473 days agobenjjneb.github.io - The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each sample. The DADA2...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 101 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 1433 days agogithub.com - The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short...
