BOL: Related items

VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse viral or other heterogeneous populations.

biogeek — Tue, 25 Aug 2020 03:40:17 -0500

VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage.

http://software.broadinstitute.org/viral/docs/vicuna_v1.0.pdf

Address of the bookmark: https://www.broadinstitute.org/viral-genomics/vicuna

GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.

Jit — Fri, 05 Feb 2021 21:22:24 -0600

GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

https://www.biorxiv.org/content/biorxiv/early/2021/02/01/2021.01.29.428779.full.pdf

Address of the bookmark: https://github.com/nadegeguiglielmoni/GraphUnzip

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

Spades tutorial PDF

Abhimanyu Singh — Tue, 01 Feb 2022 04:56:43 -0600

SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets.

Bioinformatics tools for genome assembly !

BioStar — Mon, 24 Jul 2023 07:04:26 -0500

There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:

SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.
ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.
Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.
SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.
MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.
Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.
Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.
SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.
SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.
Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.
Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.
wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.
Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.
Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.
CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.
Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.

Abhi — Sat, 08 Jun 2024 15:54:36 -0500

quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.

Task include:

AssemblyMapper : reference-guided genome assembly
GapFiller : long-reads based gap filling
TeloExplorer : telomere identification
CentroMiner : centromere candidate prediction

https://academic.oup.com/hr/article/10/8/uhad127/7197191?login=false

Address of the bookmark: http://www.atcgn.com:8080/quarTeT/home.html

MAKER

Jitendra Narayan — Sun, 07 Feb 2016 15:59:24 -0600

MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

More at http://www.yandell-lab.org/software/maker.html

Address of the bookmark: http://www.yandell-lab.org/software/maker.html

CrossMap

Jitendra Narayan — Mon, 08 Feb 2016 15:47:00 -0600

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).

It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.

We do not recommend using CrossMap to convert genome coordinates between species.

More at http://crossmap.sourceforge.net/

Address of the bookmark: http://crossmap.sourceforge.net/

Easyfig

Poonam Mahapatra — Fri, 29 Apr 2016 05:49:39 -0500

Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/

QUAST: quality assessment tool for genome assemblies

Jitendra Prajapati — Wed, 06 Apr 2016 18:23:33 -0500

QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.
It can works both with and without a given reference genome.
The tool accepts multiple assemblies, thus is suitable for comparison.

More at http://bioinf.spbau.ru/quast

http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long