Jit
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Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2226 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...
Evaluation of genome assembly software based on long reads
By BioStar 2121 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1757 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2809 days agoStructural variation caller tools using long readsTAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2384 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2226 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...Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 1750 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
By Rahul Nayak 1653 days agogithub.com - LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2257 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...wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
By BioStar 2118 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly...
