OrthoANI: An improved algorithm and software for calculating average nucleotide identity
OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share th...nterface that allow researchers to calculate OrthoANI values between genomes of int...2035 days ago
KEGG Mapper – Reconstruct Pathway
Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multip...2035 days ago
2035 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 a...2030 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 sequenc...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 frequently detected between allelic haplotypes a...affolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes. ALLHI...2026 days ago
Genome Annotation using MAKER tutorial !
MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predic...ing. Here I will describe a de novo genome annotation for Boa const...s easy to use this as a guide to annotate any genome.2026 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...n the assembly completeness and contiguity for a given genome and set...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 hypotheses. For example, histone modi...lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide en...2019 days ago