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/

Assembly Course

Shruti Paniwala — Mon, 10 Jul 2017 09:38:05 -0500

https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

Address of the bookmark: https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

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/

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

Opera: An optimal genome scaffolding program

Jit — Mon, 27 Nov 2017 10:18:20 -0600

Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes.

Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y.

Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

Address of the bookmark: https://sourceforge.net/projects/operasf/

Scripts for the analysis of HGT in genome sequence data.

Jit — Wed, 29 Nov 2017 16:44:10 -0600

Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt

Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Jit — Tue, 26 Dec 2017 22:23:39 -0600

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

List of visualization tools for genome alignments

Rahul Nayak — Fri, 02 Feb 2018 13:25:33 -0600

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. But sometime, we need publication ready figure of genomes. Following are the list of genome alignment visualization tools, which could be useful for analysis and interpretation of results:

ABySS Explorer

Interactive Java application that uses a novel graph-based representation to display a sequence assembly and associated metadata

http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer

BamView

Genome browser and annotation tool that allows visualization of sequence features, next-generation sequencing (NGS) data and the results of analyses within the context of the sequence, and also its six-frame translation

http://www.sanger.ac.uk/resources/software/artemis/

DNannotator

Annotation web toolkit for regional genomic sequences

http://bioapp.psych.uic.edu/DNannotator.htm

JVM

Java Visual Mapping tool for NGS reads

http://www.springer.com/cda/content/document/cda_downloaddocument/9789401792448-c2.pdf?SGWID=0-0-45-1487072-p176815501

LookSeq

Web-based visualization of sequences derived from multiple sequencing technologies. Low- or high-depth read pileups and easy visualization of putative single nucleotide and structural variation

http://lookseq.sourceforge.net

MagicViewer

Visualization of short read alignment, identification of genetic variation and association with annotation information of a reference genome

http://bioinformatics.zj.cn/magicviewer/

MapView

Alignments of huge-scale single-end and pair-end short reads

http://omictools.com/mapview-s1367.html

MultiPipMaker

Computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ‘percent identity plot’ (pip)

http://pipmaker.bx.psu.edu/pipmaker/

PileLineGUI

Handling genome position files in NGS studies

http://sing.ei.uvigo.es/pileline/pilelinegui.html

SAMtools tview

Simple and fast text alignment viewer; NGS compatible

http://www.htslib.org/

SEWAL

Uses a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run

http://www.sourceforge.net/projects/sewal

STAR

A web-based integrated solution to management and visualization of sequencing data

http://wanglab.ucsd.edu/star/browser

SVA

Software for annotating and visualizing sequenced human genomes

http://www.svaproject.org

Viewer (IGV)

Visualization of large heterogeneous datasets, providing a smooth and intuitive user experience at all levels of genome resolution

https://www.broadinstitute.org/igv/

ZOOM Lite

NGS data mapping and visualization software

http://bioinfor.com/zoom/lite/