BOL: Related items

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Jit — Mon, 17 Feb 2020 05:38:46 -0600

Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.

Address of the bookmark: http://catchenlab.life.illinois.edu/chromonomer/

truvari: Structural variant comparison tool for VCFs

Jit — Tue, 30 Jun 2020 21:30:44 -0500

Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

Clustergrammer is a web-based tool for visualizing high-dimensional data as an interactive and shareable hierarchically clustered heatmap

BioStar — Sun, 23 Aug 2020 19:30:17 -0500

Clustergrammer is a web-based tool for visualizing high-dimensional data (e.g. a matrix) as an interactive and shareable hierarchically clustered heatmap. Clustergrammer's front end (Clustergrammer-JS) is built using D3.js and its back-end (Clustergrammer-PY) is built using Python. Clustergrammer produces highly interactive visualizations that enable intuitive exploration of high-dimensional data and has several biology-specific features (e.g. enrichment analysis, see Biology-Specific Features) to facilitate the exploration of gene-level biological data.

Address of the bookmark: https://github.com/MaayanLab/clustergrammer

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

Neel — Wed, 23 Jun 2021 07:54:53 -0500

LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Jit — Wed, 29 Jun 2022 03:22:26 -0500

InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

Address of the bookmark: http://www.interactivenn.net/

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

LoVis4u: Locus Visualisation tool for comparative genomics

LEGE — Tue, 17 Sep 2024 02:30:57 -0500

Description

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

Address of the bookmark: https://github.com/art-egorov/lovis4u

IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer

Jit — Thu, 23 Nov 2017 10:24:19 -0600

This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It includes a functions to generate a number plots for examining the statistics that we think will be useful for this task.

However, nanopore sequencing is an emerging and rapidly developing technology. It is not clear what will be most informative. We hope that IONiseR will provide a framework for visualisation of metrics that we haven’t thought of, and welcome feedback at mike.smith@embl.de.

If you’re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final section of this document.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html

Referee: Genome assembly quality scores

Jit — Sun, 04 Nov 2018 16:44:30 -0600

Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly.

We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.

Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.

https://github.com/gwct/referee

Address of the bookmark: https://gwct.github.io/referee/#

Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data

Jit — Thu, 11 Feb 2021 21:39:05 -0600

Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim