BOL: Related items

TRITEX sequence assembly pipeline for Triticeae genomes

Jit — Tue, 20 Aug 2019 09:47:14 -0500

The pipeline is open-source and hosted in a public Bitbucket repository.

TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a BAC-by-BAC assembly. It has never been tested and is not expected to work on heterozygous or autopolyploid genomes.

A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium data.

Address of the bookmark: https://tritexassembly.bitbucket.io/

Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Jit — Sun, 31 May 2020 01:59:30 -0500

Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for assembly.

Supernova should be run using 38-56x coverage of the genome.
• Somewhat higher coverage is sometimes advantageous.
• Supernova will exit if it finds that coverage is far from the recommended range.
• Note that at most 2.14 billion reads are allowed.
• Please note that we have not extensively tested genomes larger than human, and any genome above approximately 4 GB should be considered experimental and is not supported.

Address of the bookmark: https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/running

auN: a new metric to measure assembly contiguity

Jit — Tue, 02 Aug 2022 01:18:47 -0500

Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A longer N50 indicates better contiguity. We can similarly define Nx such that contigs no shorter than Nx covers x% of the assembly. The Nx curve plots Nx as a function of x, where x is ranged from 0 to 100.

Address of the bookmark: https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

REAPR: a universal tool for genome assembly evaluation

Jitendra Prajapati — Wed, 06 Apr 2016 18:26:31 -0500

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.

http://www.sanger.ac.uk/science/tools/reapr

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-5-r47

GAEMR

Jit — Tue, 14 Jun 2016 06:18:37 -0500

The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete analysis report, or executed individually to generate specific charts and tables. GAEMR standardizes input by converting a variety of read types to Binary Alignment Map (BAM) format, allowing a single input format to be entered into GAEMR’s analysis pipeline, hence enabling the generation of standard reports.

GAEMR’s analysis philosophy is centered on contiguity, correctness, and completeness -- how many pieces in an assembly composed of, how well those pieces accurately represent the genome sequenced, and how much of that genome is represented by those pieces. By performing over twenty different analyses based on these principles, GAEMR gives a clear picture of the condition of a genome assembly.

Address of the bookmark: https://www.broadinstitute.org/software/gaemr/

SWALO

Jit — Wed, 30 Nov 2016 05:06:05 -0600

SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

Download

Git repository of SWALO is at https://github.com/atifrahman/SWALO.

Address of the bookmark: https://atifrahman.github.io/SWALO/

HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution

Jit — Wed, 07 Feb 2018 09:40:22 -0600

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"

Preprint: http://biorxiv.org/content/early/2016/08/01/062117
Paper: http://genome.cshlp.org/content/27/5/747.full
An ipython notebook to reproduce results in the paper can be found in this repository.

HINGE is an OLC(Overlap-Layout-Consensus) assembler. The idea of the pipeline is shown below.

Address of the bookmark: https://github.com/HingeAssembler/HINGE

SPADes team announce new version SPADes v3.15

BioStar — Fri, 15 Jan 2021 10:24:27 -0600

New SPAdes 3.15.0.0. announced by the SPADes team This release includes such new features as:
- CoronaSPAdes pipeline for the assembly of transcriptomic and metatranscriptomic data of full-length coronaviridae genomes;
- Meta-Viral and RNA-Viral pipelines for metagenomic and metatranscriptomic data defining viral genomes;
-New trusted contiguous use algorithm;
-Switched to the memory allocator mimalloc;
- PlasmidSPAdes and bgcSPAdes are now provided as an input assembly graph;
- Important improvements and corrections to the metaplasmid pipeline;
- Multiple performance improvements in procedures for simplification and repeat resolving.
Please, consider updating.

Check out more at https://cab.spbu.ru/software/spades/

MGRA: Breakpoint graphs and ancestral genome reconstructions

Jit — Tue, 25 Jul 2017 08:48:25 -0500

MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes.

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

Address of the bookmark: http://mgra.cblab.org/