BOL: Related items

gbtools: Interactive Visualization of Metagenome Bins in R

Jit — Sun, 26 Mar 2017 15:41:31 -0500

We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other.

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

Genome Annotation Transfer Utility (GATU)

Jit — Mon, 29 May 2017 05:54:53 -0500

Genome Annotation Transfer Utility (GATU) was designed to facilitate quick, efficient annotation of similar genomes using genomes that have already been annotated. For example, whenever a new strain of SARS coronavirus is sequenced, it is possible, using GATU, to automatically annotate the new strain using a previously-annotated strain of SARS CoV. This saves researchers from tedious manual annotation of these sequences.

The program utilizes tBLASTn and BLASTn algorithms to map genes from the reference genome (the annotated strain) to the new sequence (the unannotated strain). The goal is to annotate the majority of the new genome’s genes in a single step. ORFs present in the target genome and absent from the reference genome are also identified; these ORFs can be further analyzed using BLAST, VGO and BBB. Afterwards, they can either be accepted for/rejected from annotation. GATU can handle multiple-exon genes as well as mature peptides. Although it was designed for use with viral genomes, GATU can also be used to help annotate larger genomes (ie. bacterial genomes).

The output is saved in GenBank, XML, or EMBL file format.

Address of the bookmark: https://virology.uvic.ca/help/tool-help/help-books/genome-annotation-transfer-utility-gatu-documentation/

funannotate: Eukaryotic Genome Annotation Pipeline

Jit — Wed, 19 Sep 2018 07:47:22 -0500

Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require significant manually editing to comply with GenBank submission rules, thus funannotate is aimed at simplifying the genome submission process.

Address of the bookmark: https://github.com/nextgenusfs/funannotate

Earth BioGenome Project

Jit — Wed, 25 Apr 2018 07:48:56 -0500

The central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi and other organisms whose cells have a nucleus that houses their chromosomal DNA. To date, the genomes of less than 0.2 percent of eukaryotic species have been sequenced.

More at https://www.ucdavis.edu/news/earth-biogenome-project-aims-sequence-dna-all-complex-life

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

pWhatsHap: a parallel, high-performance version of WhatsHap

Jit — Wed, 14 Nov 2018 08:20:27 -0600

Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standard file formats. Building on WhatsHap, pWhatsHap exhibits the same complexity exploring a number of possible solutions which is exponential in the coverage of the dataset. The parallel implementation on multi-core architectures allows for a relevant reduction of the execution time for haplotyping, while the provided results enjoy the same high accuracy as that provided by WhatsHap, which increases with coverage.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1170-y

Address of the bookmark: https://bitbucket.org/whatshap/whatshap

gVolante: Completeness Assessment of Genome/Transcriptome Sequences

Neel — Sun, 13 Jan 2019 07:03:25 -0600

A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section

Address of the bookmark: https://gvolante.riken.jp/analysis.html

gEVAL: Genome Evaluation Browser

Jit — Tue, 18 Jun 2019 05:39:08 -0500

The gEVAL Browser allows the evaluation of genome assemblies through its tools and pre-computed analyses.

The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assist in strategizing potential solutions for these issues.

This facilitates the improvement of overall assemblies to a “gold” standard for release as reference genomes

Address of the bookmark: https://geval.sanger.ac.uk/index.html

Genome in a Bottle (GIAB) Consortium

Jit — Sat, 25 Jan 2020 13:50:52 -0600

The Genome in a Bottle (GIAB) Consortium is a public-private-academic consortium hosted by NIST to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome sequencing to clinical practice.

https://www.nist.gov/news-events/news/2016/09/nist-releases-new-family-standardized-genomes

Address of the bookmark: https://jimb.stanford.edu/giab/

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Neel — Sun, 20 Dec 2020 01:39:54 -0600

The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Described by Alser et al. (preliminary version at https://arxiv.org/abs/1910.09020).

Address of the bookmark: https://github.com/CMU-SAFARI/SneakySnake