BOL: Related items

Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data

Neel — Fri, 25 Feb 2022 04:42:09 -0600

This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Jit — Tue, 14 Nov 2017 10:26:16 -0600

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

Jit — Fri, 29 Jun 2018 09:19:56 -0500

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry https://jbrowse.org/

Address of the bookmark: https://github.com/GMOD/jbrowse

AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome

Jit — Mon, 23 Dec 2019 10:20:13 -0600

We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

Address of the bookmark: https://github.com/CMU-SAFARI/AirLift

Genome Workbench 2.10.7

Gudiya Pal — Fri, 01 Jul 2016 12:09:59 -0500

Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

BLAST Tool: added support for local custom BLAST databases
Graphical Sequence View: added log scaling option for graph tracks
Generic Table View: new tutorial added

Bug Fixes and Improvements

Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
Tree View: layout updated to better accommodate nodes of different sizes
Table Import Dialog (MacOS): fixed issue with table visibility
Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
Graphical Sequence View: fixed protein coloration methods
Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
Search View: ORF Finder – fixed incorrect protein lengths
Fixed bug with not opening project file (.gbp) on a click
Fixed issues in GVF import
Fixed BLAST Search tool against NCBI databases not working
Fixed tblastn (protein BLAST) not working in standalone mode
Fixed GTF export failure

VAGUE:Velvet Assembler Graphical Front End

Jit — Fri, 24 Feb 2017 08:56:49 -0600

VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginners to use, but VAGUE makes it clear and simple

More at http://www.vicbioinformatics.com/software.vague.shtml

Address of the bookmark: http://www.vicbioinformatics.com/software.vague.shtml

RepeatModeler

Jit — Thu, 18 Aug 2016 09:57:15 -0500

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

Address of the bookmark: http://www.repeatmasker.org/RepeatModeler.html

TGNet

Shruti Paniwala — Wed, 24 Aug 2016 05:36:36 -0500

Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis.

Visualization and quality assessment of de novo genome assemblies

Citation

This software is fully described in the paper:
Riba-Grognuz, Keller, Falquet, Xenarios & Wurm (2011) Visualization and quality assessment of de novo genome assemblies.

In brief, our scripts create Cytoscape files to visualize transcript evidence that suggests adjacency between scaffolds and contigs.

Software requirements

BLAT (tested with Standalone BLAT v. 32×1). Source Binaries .
Cytoscape (tested with versions 2.7.0, 2.8.2)
a UNIX machine (tested on Mac OS X 10.6 and CentOS 4.6)

Address of the bookmark: https://github.com/ksanao/TGNet

Useful Bioinformatics Tools

Poonam Mahapatra — Mon, 29 Aug 2016 04:08:12 -0500

Collections of few handy tools for bioinformatician

http://molbiol-tools.ca/Convert.htm

Address of the bookmark: http://molbiol-tools.ca/Convert.htm

BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

Jit — Thu, 01 Sep 2016 08:02:59 -0500

Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.

http://www.ncbi.nlm.nih.gov/pubmed/26559507

Address of the bookmark: http://bioinf.uni-greifswald.de/bioinf/braker/