PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and method...structure variation, gene distribution with different conservative levels, and gene...2307 days ago
Circoletto: visualizing sequence similarity with Circos
Circoletto, an online visualization tool based on Circos, which provides a fast, aesth...lts. Online version and downloadable software package for offline use (source code in PERL) freely available at&...2290 days ago
Generate interactive codon usage plots
Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demo2272 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined...ST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs from other sp...863 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 huma...1552 days ago
2234 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Usin...2223 days ago
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kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates...ng reads. It is able to calculate the genetic dissimilarity between samples...bling one. De novo estimates of gene...2182 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parent...bsp;for the assembly. Trinity components should be merged with cap3. Our code to perform the merging is ava...2180 days ago