BOL: Related items

Synima: a Synteny imaging tool for annotated genome assemblies

Abhimanyu Singh — Tue, 30 Oct 2018 10:49:13 -0500

Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

BioJoker — Sun, 20 Jan 2019 06:34:36 -0600

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.

Address of the bookmark: https://github.com/shinout/clipcrop

Minipolish: A tool for Racon polishing of miniasm assemblies

BioStar — Tue, 03 Dec 2019 02:40:54 -0600

Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

Adding read depth information to contigs
Fixing sequence truncation that can occur in Racon
Adding circularising links to circular contigs if not already present (so they display better in Bandage)
'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

HASLR: a tool for rapid genome assembly of long sequencing reads

LEGE — Fri, 31 Jan 2020 05:50:15 -0600

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.

Address of the bookmark: https://github.com/vpc-ccg/haslr

GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Neel — Sun, 15 Mar 2020 03:41:12 -0500

GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

GSP4PDB is part of the services provided by the Bioinformatic Group of the University of Talca

http://gdblab.com/gsp4pdb/gsp4pdb2/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3352-x

Address of the bookmark: http://gdblab.com/gsp4pdb/gsp4pdb2/

Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies

Jit — Tue, 30 Jun 2020 21:40:52 -0500

Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome.

Address of the bookmark: https://github.com/agshumate/Liftoff

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

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations

Neel — Thu, 19 May 2022 04:29:05 -0500

The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

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