BOL: Related items

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/

Cutadapt

Bulbul — Wed, 14 Dec 2016 09:59:52 -0600

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

Cutadapt comes with an extensive suite of automated tests and is available under the terms of the MIT license.

If you use cutadapt, please cite DOI:10.14806/ej.17.1.200 .

More at https://github.com/marcelm/cutadapt

Address of the bookmark: http://cutadapt.readthedocs.io/en/stable/guide.html

A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

Abhimanyu Singh — Fri, 12 May 2017 10:50:29 -0500

PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed:

ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference.

IMAGE, an iterative approach for closing gaps in assembled genomes using mate pair information. It is able to close gaps left open by the assembler in a draft genome, even when using the same data sets as used by the original assembler.

iCORN, that enables errors in the consensus sequence to be corrected by iteratively mapping reads to the current assembly. An improved version, especially correction Pacfic Bioscience assemblies (PacBio) can be found here.

RATT, a tool to transfer the annotation from a reference genome, or an earlier assembly, onto the latest assembly.

PAGIT bundles these software and makes them more accessible for users.

Address of the bookmark: http://www.sanger.ac.uk/science/tools/pagit

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

EvidentialGene: tr2aacds, mRNA Transcript Assembly Software

Rahul Nayak — Tue, 08 May 2018 04:39:39 -0500

EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see
http://arthropods.eugenes.org/EvidentialGene/

Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. All software developed for EvidentialGene is publicly available. See project wiki/blog for notes.

Download

http://arthropods.eugenes.org/EvidentialGene/trassembly.html

https://sourceforge.net/p/evidentialgene/blog/

Address of the bookmark: http://arthropods.eugenes.org/EvidentialGene/trassembly.html

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/

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/

New born babies get ready to know their whole genome soon!!!

Rahul Agarwal — Thu, 05 Sep 2013 07:24:02 -0500

USA launch a pilot projects to examine medical information of newborn baby, which are being funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.

Awards of $5 million to four grantees have been made in fiscal year 2013 under the Genomic Sequencing and Newborn Screening Disorders research program. The program will be funded at $25 million over five years, as funds are made available.

"Hundreds of US babies will be pioneers in genomic medicine through a US$25-million programme to sequence their genomes soon after they are born."

Source:

http://blogs.nature.com/news/2013/09/scientists-to-sequence-hundreds-of-newborns-genomes.html

http://www.genome.gov/27554919

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

Ribbon: Visualizing complex genome alignments and structural variation:

Jit — Wed, 29 Nov 2017 07:40:22 -0600

Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right.

Local installation:

You can install Ribbon locally from Github by following the instructions here: https://github.com/MariaNattestad/Ribbon

Address of the bookmark: http://genomeribbon.com/