BOL: Related items

PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

BioStar — Thu, 13 Aug 2020 09:57:24 -0500

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes.

PANNZER2 processes bacterial proteomes in minutes and eukaryotic proteomes in an hour. You can use AAI-profiler to summarize a proteome's species neighbors and reveal taxonomic identity or contamination.

Address of the bookmark: http://ekhidna2.biocenter.helsinki.fi/sanspanz/#

SeqMule: Automated human exome/genome variants detection

BioStar — Tue, 18 Feb 2020 03:22:54 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.

Address of the bookmark: https://doc-openbio.readthedocs.io/projects/seqmule/en/latest/

BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus

Jit — Wed, 24 Oct 2018 23:35:09 -0500

BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads.

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

CNIDARIA: fast, reference-free phylogenomic clustering

Shruti Paniwala — Thu, 16 Jun 2016 17:55:17 -0500

Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.

Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.

Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria.

Contact: Saulo Aflitos - sauloal@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Address of the bookmark: https://github.com/sauloal/cnidaria/wiki

jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

Abhimanyu Singh — Fri, 26 Jul 2019 00:58:12 -0500

jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

Abhimanyu Singh — Tue, 30 Oct 2018 10:46:28 -0500

VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783527/

GTDB-Tk: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Rahul Nayak — Wed, 22 Aug 2018 03:21:01 -0500

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

GTDB-Tk is under active development and validation. Please independently confirm the GTDB-Tk predictions by manually inspecting the tree and bringing any discrepencies to our attention. Notifications about GTDB-Tk releases will be available through the ACE Twitter account (https://twitter.com/ace_uq).

Address of the bookmark: https://github.com/Ecogenomics/GTDBTk

‘dockr’: the R container

Jit — Mon, 23 Dec 2019 09:56:49 -0600

dockr 0.8.6 is now available on CRAN. dockr is a minimal toolkit to build a lightweight Docker container image for your R package, in which the package itself is available. The Docker image seeks to mirror your R session as close as possible with respect to R specific dependencies. Both dependencies on CRAN R packages as well as local non-CRAN R packages will be included in the Docker container image.

If you want to know, how Docker works, and why you should consider using Docker, please take a look at the Docker website.

Address of the bookmark: https://www.docker.com/why-docker

PaReBrick: PArallel REarrangements and BReaks identification toolkit

Jit — Fri, 08 Oct 2021 10:20:03 -0500

PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved.We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab691/6380551

Address of the bookmark: https://github.com/ctlab/parallel-rearrangements