BOL: All site bookmarks

Minda: a tool for evaluating structural variant (SV) callers

LEGE — Sun, 31 Mar 2024 02:43:50 -0500

Minda is a tool for evaluating structural variant (SV) callers that

standardizes VCF records for compatibility with both germline and somatic SV callers,
benchmarks against a single VCF input file, or
benchmarks against an ensemble call set created from multiple VCF input files.

Address of the bookmark: https://github.com/KolmogorovLab/minda

Severus: a somatic structural variation (SV) caller for long reads

LEGE — Sun, 31 Mar 2024 02:41:27 -0500

Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus takes advantage of long-read phasing and uses the breakpoint graph framework to model complex chromosomal rearrangements.

If you use Severus, please cite https://www.medrxiv.org/content/10.1101/2024.03.22.24304756v1

Address of the bookmark: https://github.com/KolmogorovLab/Severus

GraphPath: A graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network

LEGE — Wed, 27 Mar 2024 20:51:21 -0500

Achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels. In this paper, we present GraphPath, a biological knowledge-driven graph neural network with multi-head self-attention mechanism that implements the pathway-pathway interaction network. We train GraphPath to classify the cancer status of patients with prostate cancer based on their multi-omics profiling.

Address of the bookmark: https://github.com/amazingma/GraphPath

ExRec: Exclusion of Recombined DNA

LEGE — Wed, 27 Mar 2024 20:48:26 -0500

ExRec (Exclusion of Recombined DNA) is a Python pipeline that implements the four-gamete test to filter out recombined DNA sites from up to thousands of DNA sequence loci. The pipeline consists of five standalone applications: the first two convert folders of NEXUS or PHYLIP files into the standard input file for the main program that conducts the four-gamete filtering procedures. The pipeline outputs recombination-filtered data in concatenated NEXUS and PHYLIP formats and a tab-delimited table containing descriptive statistics for all loci and the results. This software also allows the user to output the longest non-recombined sequence blocks from loci (current best practice) or randomly select non-recombined blocks from loci (a newer approach). Two other applications in the package convert the recombination-filtered data into single-locus NEXUS or PHYLIP files. The ExRec package can thus facilitate species delimitation, species tree, and historical demography studies by providing loci that better meet the no-recombination assumption in coalescent-based analyses.

Link to the article: https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad174/7455250?searchresult=1

Link to the software:
https://github.com/Sammccarthypotter/ExRec

Address of the bookmark: https://github.com/Sammccarthypotter/ExRec

CGView.js is a Circular Genome Viewing tool

LEGE — Wed, 27 Mar 2024 11:16:24 -0500

CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView.

CGView.js is the genome viewer of Proksee, an expert system for genome assembly, annotation and visualization.

Features

Circular and linear views of genomes
Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs
Smooth zooming down to the sequence level
Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)
Save high resolution PNG maps up to 8000x8000px
Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

Proksee

LEGE — Wed, 27 Mar 2024 11:11:54 -0500

Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

Please Cite the Following

Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, Graham M, Van Domselaar G, and Stothard P

Proksee: in-depth characterization and visualization of bacterial genomes

Nucleic Acids Research, 2023, gkad326, https://doi.org/10.1093/nar/gkad326

Address of the bookmark: https://proksee.ca/

R Package for PCA Analysis

LEGE — Sun, 24 Mar 2024 20:06:24 -0500

An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on GitHub: https://github.com/Devashish13/PopulationStructure

Address of the bookmark: https://rpubs.com/Devashish13/PCAGenomics

bacLIFE: an automated genome mining tool for identification of lifestyle associated genes

BioStar — Fri, 15 Mar 2024 04:59:14 -0500

bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gene clusters associated with each lifestyle detected. This whole process is divided into different modules:

Clustering module Predicts, clusters and annotates the genes of every input genome
Lifestyle prediction Employs a machine learning model to forecast bacterial lifestyle or other specified metadata
Analitical module (Shiny app) Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.

You can find the complete wiki here [https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki]

Address of the bookmark: https://github.com/Carrion-lab/bacLIFE

UniAligner: a parameter-free framework for fast sequence alignment

Abhi — Fri, 08 Mar 2024 23:36:12 -0600

UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches, such as the Smith-Waterman algorithm, that work well for most sequences, fail to construct biologically adequate alignments of extra-long tandem repeats (ETRs), such as human centromeres and immunoglobulin loci. This limitation was overlooked in the previous studies since the sequences of the centromeres and other ETRs across multiple genomes only became available recently.

More at https://www.nature.com/articles/s41592-023-01970-4

Address of the bookmark: https://github.com/seryrzu/unialigner

doubletrouble: identify duplicated genes from whole-genome protein sequences and classify

LEGE — Tue, 05 Mar 2024 00:23:49 -0600

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/html/doubletrouble.html