ARCS: scaffolding genome drafts with linked reads
ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)Tags: ARCS, scaffolding, genome, drafts, linked, reads
1958 days ago
Versatile genome assembly evaluation with QUAST-LG
QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large ...Tags: Versatile, genome, assembly, evaluation, QUAST-LG
1954 days ago
Hawkeye: an interactive visual analytics tool for genome assemblies
Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an a...Tags: Hawkeye, interactive, visual, analytics, tool, genome, assemblies, visualization
1943 days ago
GenomeView: genome browser and annotation editor
GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.This project has moved to GitHub: https://github.com/GenomeV...Tags: GenomeView, genome, browser, annotation, editor
1943 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR ...Tags: LTR_Finder, efficient, program, find, full-length, LTR, retrotranspsons, genome, sequences
1932 days ago
Tags: LTR_retriever, accurately, identifies, annotates, LTR, retrotransposons, LAI, evaluates, continuity, genome, assemblies.
1932 days ago
Tags: CAUSEL, epigenome, genome, editing, pipeline, function, noncoding, GWAS, variants
1846 days ago
GMASS: a novel measure for genomeassembly structural similarity
The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-zTags: GMASS, novel, measure, genome, assembly, structural, similarity
1840 days ago
Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
Apollo is a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’. ...Tags: Apollo, collaborative, genomic, annotation, editor, Web, genome
1793 days ago
Tags: Cogent, tool, reconstruct, coding, genome, high-quality, full-length, transcriptome, sequences, genome, evaluation
1776 days ago