2034 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate p...2029 days ago
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)2029 days ago
FGENESH - Program for predicting multiple genes in genomic DNA sequences
FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was c...2026 days ago
ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
The major problem of scaffolding polyploid genome is that Hi-C signals are frequ...together. To solve the problem, we developed a new Hi-C scaffolding pipeline, calle...ALLHIC, specifically tailored to the polyploid genomes. ALLHIC pipeline contains a...2026 days ago
Genome Annotation using MAKER tutorial !
MAKER is a great tool for annotating a reference genome using empirical and ab initiogene pre.... Here I will describe a de novo genome annotation for Boa const...asy to use this as a guide to annotate any genome.2026 days ago
Versatile genome assembly evaluation with QUAST-LG
...ntended for evaluating large-scale genome assemblies (up to mammalia...your command! A short list of the new features (see CHANGES&nb...eedup achieved by both use of new fast aligner (minimap2) and the...ss and contiguity for a given genome and set of reads)...2025 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypothe...on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped...2019 days ago
2015 days ago
Hawkeye: an interactive visual analytics tool for genome assemblies
Genome sequencing remains an inexact science, and genome sequences ca...are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid i...p://amos.sourceforge.net/hawkeye. https://genomebiology.biomedcentral.com/arti...2014 days ago