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rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2873 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2823 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...HairSplitter: assembling long reads in an unknown number of haplotypes
By BioStar 1337 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...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 3011 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2920 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...cutadapt
By Radha Agarkar 3736 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 2381 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtgSearch: a fast and flexible general search tool for whole-genome sequencing
By Jit 2920 days agoml.ssu.ac.kr - gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...Genobuntu: A software package containing more than 70 software and packages oriented towards NGS...
By BioStar 2794 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2747 days agoamos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...
