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LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
By Rahul Nayak 1684 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...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2300 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2257 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 2152 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 1788 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...HairSplitter: assembling long reads in an unknown number of haplotypes
By BioStar 747 days agohal.archives-ouvertes.fr - Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: Very modular, can be used with any assembler Naive: makes no...LoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 2814 days agowww.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 2544 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2400 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2218 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...
