BOL: Related items

RepeatModeler2: automated genomic discovery of transposable element families

Neel — Mon, 02 Dec 2019 06:52:29 -0600

RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, https://github.com/Dfam-consortium/TETools).

Address of the bookmark: https://github.com/Dfam-consortium/TETools

gget

BioStar — Sat, 01 Apr 2023 09:42:07 -0500

gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

Address of the bookmark: https://github.com/pachterlab/gget

destruct

Jitendra Prajapati — Mon, 29 Feb 2016 17:34:59 -0600

Destruct is a tool for joint prediction of rearrangement breakpoints from single or multiple tumour samples.

More at https://bitbucket.org/dranew/destruct

Address of the bookmark: https://bitbucket.org/dranew/destruct

Synteny and Rearrangement Identifier (SyRI)

Jit — Tue, 05 May 2020 10:37:10 -0500

SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions.

Address of the bookmark: https://schneebergerlab.github.io/syri/

Tree illustrating the lack of interchromosomal rearrangement of the microchromosomes.

BioJoker — Mon, 26 Nov 2018 04:20:33 -0600

Tree illustrating the lack of interchromosomal rearrangement of the microchromosomes. No interchromosomal microchromosome fusions from the avian ancestor unless otherwise stated (macrochromosomal fusions not listed). The overall pattern of microchromosome stability and rearrangement across the species is illustrated

Jarvis et al. (2014)

Reference https://link.springer.com/article/10.1007/s00412-018-0685-6

Recombination detection tool

Jit — Tue, 02 Feb 2016 10:11:14 -0600

A program to detect recombination hotspots using population genetic data.

More at https://github.com/auton1/LDhot

Address of the bookmark: https://github.com/auton1/LDhot

RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes

Abhi — Wed, 27 Apr 2016 11:07:59 -0500

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

More at http://www.nature.com/articles/srep08365

Address of the bookmark: http://rast.nmpdr.org/

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Neel — Fri, 20 May 2016 18:53:49 -0500

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581

GAEMR

Jit — Tue, 14 Jun 2016 06:18:37 -0500

The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete analysis report, or executed individually to generate specific charts and tables. GAEMR standardizes input by converting a variety of read types to Binary Alignment Map (BAM) format, allowing a single input format to be entered into GAEMR’s analysis pipeline, hence enabling the generation of standard reports.

GAEMR’s analysis philosophy is centered on contiguity, correctness, and completeness -- how many pieces in an assembly composed of, how well those pieces accurately represent the genome sequenced, and how much of that genome is represented by those pieces. By performing over twenty different analyses based on these principles, GAEMR gives a clear picture of the condition of a genome assembly.

Address of the bookmark: https://www.broadinstitute.org/software/gaemr/

EasyBuild

Jit — Fri, 27 Jan 2017 16:00:43 -0600

EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/