Jit
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Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2696 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...FSA: Fast Statistical Alignment
By Jit 3316 days agofsa.sourceforge.net - FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a...RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
By BioJoker 2515 days agogithub.com - Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into...DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
By Jit 1942 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...Mash: fast genome and metagenome distance estimation using MinHash
By Jit 3007 days agogithub.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2844 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,...Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 2315 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 2067 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
By Rahul Nayak 1416 days agogithub.com - PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 168 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...
