Jit
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GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 2759 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 2408 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,...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2365 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2291 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...COSINE: non-seeding method for mapping long noisy sequences
By Jit 2253 days agogithub.com - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1817 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 1734 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
By Jit 2859 days agokakitone.github.io - FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2320 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 2773 days agosourceforge.net - Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,...
