BOL: Related items

RagTag: a collection of software tools for scaffolding and improving modern genome assemblies

Jit — Sat, 11 Sep 2021 00:28:14 -0500

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

Homology-based misassembly correction
Homology-based assembly scaffolding and patching
Scaffold merging

Address of the bookmark: https://github.com/malonge/RagTag

Mitochondrial genome assembly tools !

Abhi — Wed, 06 Sep 2023 00:37:18 -0500

Mitochondrial genome assembly tools are specialized software and algorithms designed to accurately reconstruct the mitochondrial genome (mitogenome) from sequencing data, typically obtained through techniques like next-generation sequencing (NGS). The mitochondrial genome is relatively small compared to the nuclear genome, making it an ideal target for assembly. Here are some commonly used mitochondrial genome assembly tools:

MitoFinder: Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

MITObim: MITObim is a tool specifically developed for the iterative assembly of mitochondrial genomes. It starts with a reference mitogenome and iteratively refines the assembly using the read data.

MITOS: MITOS is a web-based platform that provides a pipeline for annotating mitochondrial genomes. It integrates multiple software tools for assembly, annotation, and visualization of mitogenomes.

MIRA: MIRA (Mimicking Intelligent Read Assembly) is a versatile genome assembly tool that can be used for mitochondrial genome assembly. It supports various sequencing technologies and allows for reference-based or de novo assembly.

NOVOPlasty: NOVOPlasty is a user-friendly tool designed for de novo assembly of organelle genomes, including mitochondria. It utilizes a seed-and-extend algorithm and is suitable for both short-read and long-read data.

MITOS2: MITOS2 is an updated version of the MITOS pipeline, which automates the annotation of mitochondrial genomes. It provides improved accuracy and additional features for mitochondrial genome analysis.

GetOrganelle: While primarily designed for chloroplast genome assembly, GetOrganelle can also be used for mitochondrial genome assembly. It is particularly useful for dealing with high-throughput sequencing data.

SPAdes: SPAdes (St. Petersburg genome assembler) is a versatile genome assembly tool that can be employed for mitochondrial genome assembly, especially when dealing with complex datasets that may contain nuclear mitochondrial DNA sequences (numts).

IDBA-UD: IDBA-UD (Iterative De Bruijn Graph De Novo Assembler) is another de novo assembly tool that can be used for mitochondrial genome assembly, especially in cases with relatively low coverage.

Velvet: Velvet is a de novo assembly tool that can be applied to mitochondrial genome assembly, especially when working with short-read data.

When selecting a mitochondrial genome assembly tool, it's important to consider the specific characteristics of your sequencing data, such as read length and coverage, as well as the complexity of the mitochondrial genome. Additionally, some tools are better suited for specific organisms or research objectives, so choosing the right tool will depend on your particular project requirements.

mafTools

Radha Agarkar — Sat, 21 May 2016 22:40:21 -0500

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

Address of the bookmark: https://github.com/dentearl/mafTools

sockeye

Jit — Fri, 17 Feb 2017 08:51:16 -0600

This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

bedtools

Jit — Fri, 24 Feb 2017 04:50:44 -0600

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.

Address of the bookmark: http://bedtools.readthedocs.io/en/latest/index.html

Salzberg lab

Mon, 15 May 2017 05:14:01 -0500

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

https://salzberg-lab.org/

AnchorWave

Neel — Wed, 23 Feb 2022 08:14:35 -0600

AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy and merging them together, AnchorWave generates a whole-genome alignment for each collinear block. AnchorWave implements commands to guide collinear block identification with or without chromosomal rearrangements and provides options to use known polyploidy levels or whole-genome duplications to inform alignment.

Address of the bookmark: https://github.com/baoxingsong/AnchorWave

MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly

Abhi — Sat, 08 Jun 2024 16:15:25 -0500

The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as sequence search or differential assembly.

Searcg link https://metagraph.ethz.ch/search

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4

Address of the bookmark: https://metagraph.ethz.ch/

CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms

Jit — Tue, 25 Jul 2017 05:03:10 -0500

Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized the field of bioinformatics, and is currently implemented in all free and commercial bioinformatics packages. However, with the advent of Next Generation Sequencing (NGS) and the development of new sequencing techniques, the utility of traditional BLAST implementations is limited. CrocoBLAST combines the accuracy and general applicability of BLAST with computational efficiency, accessibility, and user experience, so that NGS data can be analyzed efficiently even when only modest computational resources are available.

https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

Address of the bookmark: https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

Jit — Fri, 08 Dec 2017 16:48:40 -0600

Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to Tom Slezak for revsing the get_genbank_file3 script and to Tod Stuber (USDA) for testing version 3.1 even though he doesn't need the annotation feature. All users are encouraged to upgrade to version 3.1.

Address of the bookmark: https://sourceforge.net/projects/ksnp/files/