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ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 819 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
By Abhi 849 days agogithub.com - MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard...liftover
By Jitendra Narayan 3830 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...RNA-Seq De novo Assembly Using Trinity
By Surabhi Chaudhary 3787 days agogithub.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...DISCOVAR
By Abhimanyu Singh 3761 days agowww.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3753 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...Blobology
By Jit 3705 days agogithub.com - Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh Goal: To create blobplots or...Redundans
By Jit 3625 days agogithub.com - Redundans pipeline assists an assembly of heterozygous genomes.Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should...HGA
By Jit 3536 days agogithub.com - HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler...Standardized velvet assembly report
By Poonam Mahapatra 3526 days agogithub.com - Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate...
