BOL: Related items

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Jit — Mon, 19 Feb 2018 06:46:15 -0600

ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics.

The new features include

(i) building gene-based and supermatrix-based phylogenies using a single command,

(ii) testing and visualizing evolutionary models,

(iii) calculating distances between trees of different size or including duplications, and

(iv) providing seamless integration with the NCBI taxonomy database.

ETE is freely available at http://etetoolkit.org

Address of the bookmark: http://etetoolkit.org

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

BioJoker — Tue, 27 Nov 2018 04:43:57 -0600

lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

Address of the bookmark: https://github.com/vpc-ccg/lordfast

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/

AutoGluon: AutoML for Text, Image, and Tabular Data

Jit — Thu, 07 Jan 2021 05:33:17 -0600

AutoGluon automates machine learning tasks enabling you to easily achieve strong predictive performance in your applications. With just a few lines of code, you can train and deploy high-accuracy machine learning and deep learning models on text, image, and tabular data.

Address of the bookmark: https://github.com/awslabs/autogluon

NASA Open Science Data Repository

Abhi — Wed, 18 Dec 2024 11:54:47 -0600

The NASA Open Science Data Repository (OSDR) enables access to space-related data from experiments and missions that investigate biological and health responses of terrestrial life to spaceflight. The goal of OSDR is to enable multi-modal and multi-hierarchical fundamental space life science data be reused toward basic science, applied science, and operational outcomes for space exploration and knowledge discovery. These data include ‘omics, phenotypic, physiological, behavioral, hardware, environmental telemetry; raw, processed; tabular, text, code, bioimaging, and video.

https://www.nasa.gov/reference/osdr-data-processing/

Address of the bookmark: https://www.nasa.gov/osdr/

mafTools

Radha Agarkar — Sat, 21 May 2016 22:40:21 -0500

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

Address of the bookmark: https://github.com/dentearl/mafTools

Mercator: Multiple Whole-Genome Orthology Map Construction

Jit — Tue, 19 May 2020 16:46:22 -0500

Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous", "orthologous", and "paralogous" instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence. Here we present our initial work in the form a program called Mercator that constructs orthology maps between multiple whole genomes.

Address of the bookmark: https://www.biostat.wisc.edu/~cdewey/mercator/

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

Jit — Fri, 28 Sep 2018 09:35:10 -0500

GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

Step 1. Run mugsy to get multiple sequence alignment results.
Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

Cactus: a reference-free whole-genome multiple alignment program

Jit — Mon, 12 Aug 2019 07:52:33 -0500

Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111

Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should expect Cactus to use approximately 120 CPU-days of compute per genome, with about 120 GB of RAM used at peak. The requirements scale roughly quadratically, so aligning two 1-megabase bacterial genomes takes only 1.5 CPU-hours and 14 GB RAM.

Address of the bookmark: https://github.com/ComparativeGenomicsToolkit/cactus

SVbyEye: R Package to visualize alignments between two or multiple DNA sequences

LEGE — Tue, 17 Sep 2024 02:34:57 -0500

R Package to visualize alignments between two or multiple DNA sequences including
a number of functionalities to facilitate processing of alignments in PAF format.

SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process alignments in PAF format. The tool facilitates the characterization of complex SVs in the context of sequence homology helping resolve the mechanisms underlying their formation. Availability and implementation SVbyEye is available at https://github.com/daewoooo/SVbyEye.

Author: David Porubsky

Address of the bookmark: https://github.com/daewoooo/SVbyEye