BOL: Related items

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/

ARCS: scaffolding genome drafts with linked reads

Rahul Nayak — Tue, 06 Mar 2018 16:35:26 -0600

ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.

Address of the bookmark: https://github.com/bcgsc/ARCS/

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

Jit — Tue, 12 Jun 2018 08:14:41 -0500

P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/

getopts.pl file

Jit — Fri, 15 Jun 2018 04:43:03 -0500

SSPACE_longread complain for getopts.pl file.

To resolve this, download and have in SSPACED-Longreads folder.

Cheers :)

Nanopolis: polish a genome assembly

Rahul Nayak — Thu, 26 Jul 2018 04:51:28 -0500

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Address of the bookmark: https://github.com/jts/nanopolish

Scribl : HTML5 canvas genomics graphic library

Jit — Thu, 25 Oct 2018 09:38:53 -0500

Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.

Address of the bookmark: http://chmille4.github.io/Scribl/

swgis v2.0 : a seqword genomic island sniffer

Abhimanyu Singh — Thu, 01 Nov 2018 12:35:52 -0500

swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in the eugi database.

download swgis v2.0

Address of the bookmark: http://eugi.bi.up.ac.za/eugi_download_swgis.php

SKESA: strategic k-mer extension for scrupulous assemblies

Jit — Wed, 14 Nov 2018 04:45:41 -0600

SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources.

Source code for SKESA is freely available at https://github.com/ncbi/SKESA/releases.

Research Paper @ Link

SKESA algorithm are as follows:

Address of the bookmark: https://github.com/ncbi/SKESA/releases

Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies

Rahul Nayak — Mon, 17 Dec 2018 03:17:20 -0600

Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're working on the haploid or phased-diploid assembly.

Identify pairs of contigs that are syntenic and move one of them to the haplotig 'pool'. The pipeline uses mapped read coverage and Minimap2 alignments to determine which contigs to keep for the haploid assembly. Dotplots are optionally produced for all flagged contig matches, juxtaposed with read-coverage, to help the user determine the proper assignment of any remaining ambiguous contigs. The pipeline will run on either a haploid assembly (i.e. Canu, FALCON or FALCON-Unzip primary contigs) or on a phased-diploid assembly (i.e. FALCON-Unzip primary contigs + haplotigs). Here are two examples of how Purge Haplotigs can improve a haploid and diploid assembly.

Address of the bookmark: https://bitbucket.org/mroachawri/purge_haplotigs

GenomeView: genome browser and annotation editor

Rahul Nayak — Wed, 02 Jan 2019 04:09:06 -0600

GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This project has moved to GitHub: https://github.com/GenomeView/genomeview

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