BOL: Related items

SCUBAT: Scaffolding Contigs Using Blat And Transcripts

Rahul Nayak — Tue, 13 Mar 2018 06:52:24 -0500

SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.

Address of the bookmark: https://github.com/elswob/SCUBAT

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

Jit — Sun, 27 Oct 2019 00:57:23 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Misassembly correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

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

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

CSAR-web: a web server of contig scaffolding using algebraic rearrangements

BioStar — Fri, 10 Apr 2020 04:39:36 -0500

CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism.

CSAR-web can serve as a convenient and useful scaffolding tool allowing the users to efficiently and accurately scaffold their draft genomes according to a complete or incomplete reference genome.

Address of the bookmark: http://genome.cs.nthu.edu.tw/CSAR-web

Seal: SEquence ALignment evaluation suite

Jit — Wed, 03 Jan 2018 05:05:46 -0600

Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

Reading a pre-existing reference genome from one or more FASTA files.
Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
Applying alignment tools to the genome and the reads through a standardized interface.
Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

Bowtie
BWA
MAQ
mrFAST
mrsFAST
Novoalign
SHRiMP
SOAPv2

Address of the bookmark: http://compbio.case.edu/seal/

Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.

Jit — Tue, 18 Jun 2019 05:33:04 -0500

Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

See a recent presentation on Cogent being applied to the Cuttlefish Iso-Seq data.

Cogent preliminary draft paper (updated 2016Dec version), Supplementary

Please see wiki for details on usage.

Address of the bookmark: https://github.com/Magdoll/Cogent

Tools to Predict the Impact of Missense Variants !

Jit — Mon, 23 Apr 2018 12:57:33 -0500

Prioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and Mendelian diseases. A large number of in silico tools have been employed for the task of pathogenicity prediction, including PolyPhen‐2, SIFT, FatHMM, MutationTaster‐2, MutationAssessor, Combined Annotation Dependent Depletion, LRT, phyloP, and GERP++, as well as optimized methods of combining tool scores, such as Condel and Logit. Due to the wealth of these methods, an important practical question to answer is which of these tools generalize best, that is, correctly predict the pathogenic character of new variants.

Study of 10 tools on five datasets that such a comparative evaluation of these tools is hindered by two types of circularity: they arise due to (1) the same variants or (2) different variants from the same protein occurring both in the datasets used for training and for evaluation of these tools, which may lead to overly optimistic results. Comparative evaluations of predictors that do not address these types of circularity may erroneously conclude that circularity confounded tools are most accurate among all tools, and may even outperform optimized combinations of tools.

Following tools are useful for mis sense muation detection ...

PolyPhen‐2 (PP2)
“Predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations”

MutationTaster‐2 (MT2)
“Evaluation of the disease‐causing potential of DNA sequence alterations”

MutationAssessor (MASS)
“Predicts the functional impact of amino acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms”

LRT
“Identify a subset of deleterious mutations that disrupt highly conserved amino acids within protein‐coding sequences, which are likely to be unconditionally deleterious”

SIFT
“Predicts whether an amino acid substitution affects protein function”

GERP++
“Identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as “rejected substitutions.” Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element”

phyloP
“Compute conservation or acceleration P values based on an alignment and a model of neutral evolution”

FatHMM unweighted (FatHMM‐U)
Predicts “functional consequences of both coding variants, that is, nonsynonymous single‐nucleotide variants, and noncoding variants”

FatHMM weighted (FatHMM‐W)
Predicts “functional consequences of both coding variants, that is, nonsynonymous single‐nucleotide variants, and noncoding variants” and its weighting scheme attributes higher tolerance scores to SNVs in proteins, related proteins, or domains that already include a high fraction of pathogenic variantsh

Combined Annotation Dependent Depletion (CADD)
“CADD is a tool for scoring the deleteriousness of single‐nucleotide variants as well as insertion/deletions variants in the human genome”

SRBreak: A Read-Depth and Split-Read Framework to Identify Breakpoints of Different Events Inside Simple Copy-Number Variable Regions

Jit — Tue, 15 May 2018 04:42:11 -0500

SRBreak is a read-depth and split-read package written in R for identifying copy-number variants in next-generation sequencing datasets. Note: SBReak was designed to work for multiple samples. It can work for >= 2 samples, but we suggest that users should use >= 5 samples as in the work tested in our paper.

Address of the bookmark: https://github.com/hoangtn/SRBreak

mojolicious: a next generation web framework for the Perl programming language.

Jit — Fri, 12 Jan 2018 16:48:10 -0600

Back in the early days of the web, many people learned Perl because of a wonderful Perl library called CGI. It was simple enough to get started without knowing much about the language and powerful enough to keep you going, learning by doing was much fun. While most of the techniques used are outdated now, the idea behind it is not. Mojolicious is a new endeavor to implement this idea using bleeding edge technologies.

Features

An amazing real-time web framework, allowing you to easily grow single file prototypes into well-structured MVC web applications.
- Powerful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session management, form validation, testing framework, static file server, CGI/PSGI detection, first class Unicode support and much more for you to discover.
A powerful web development toolkit, that you can use for all kinds of applications, independently of the web framework.
- Full stack HTTP and WebSocket client/server implementation with IPv6, TLS, SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support.
- Built-in non-blocking I/O web server, supporting multiple event loops as well as optional pre-forking and hot deployment, perfect for building highly scalable web services.
- JSON and HTML/XML parser with CSS selector support.
Very clean, portable and object-oriented pure-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed)
Fresh code based upon years of experience developing Catalyst, free and open source.
Hundreds of 3rd party extensions and high quality spin-off projects like the Minion job queue.

http://mojolicious.org/

Address of the bookmark: http://mojolicious.org/

nQuire: A statistical framework for ploidy estimation using NGS short-read data

Jit — Thu, 31 Jan 2019 05:12:19 -0600

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases are segregating.

For more background see also the publication at BMC Bioinformatics.

https://github.com/clwgg/nQuire

Address of the bookmark: https://github.com/clwgg/nQuire