Jit
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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2200 days agogithub.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2129 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2061 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...StringTie Transcript assembly and quantification for RNA-Seq
By Jit 1627 days agoccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...3D de novo assembly (3D DNA) pipeline
By Jit 1755 days agogithub.com - For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly. For the original version of the pipeline and to reproduce the...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 1701 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...Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
By Jit 1637 days agosupport.10xgenomics.com - Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for...auN: a new metric to measure assembly contiguity
By Jit 844 days agolh3.github.io - Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A...The Genome 10K Project
By Jit 3769 days agohttps://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction...liftover
By Jitendra Narayan 3210 days ago Comments (1)github.com - Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at...
