BOL: Related items

Ribbon !!

Jit — Fri, 21 Oct 2016 04:54:30 -0500

Visualization has played an extremely important role in the current genomic revolution to inspect and understand variants, expression patterns, evolutionary changes, and a number of other relationships. However, most of the information in read-to-reference or genome-genome alignments is lost for structural variations in the one-dimensional views of most genome browsers showing only reference coordinates. Instead, structural variations captured by long reads or assembled contigs often need more context to understand, including alignments and other genomic information from multiple chromosomes. We have addressed this problem by creating Ribbon (genomeribbon.com) an interactive online visualization tool that displays alignments along both reference and query sequences, along with any associated variant calls in the sample. This way Ribbon shows patterns in alignments of many reads across multiple chromosomes, while allowing detailed inspection of individual reads (Supplementary Note 1). For example, here we show a gene fusion in the SK-BR-3 breast cancer cell line linking the genes CYTH1 and EIF3H. While it has been found in the transcriptome previously, genome sequencing did not identify a direct chromosomal fusion between these two genes. After SMRT sequencing, Ribbon shows that there are indeed long reads that span from one gene to the other, going through not one but two variants, for the first time showing the genomic link between these two genes (Figure 1a). More gene fusions of this cancer cell line are investigated in Supplementary Note 2. Figure 1b shows another complex event in this sample made simple in Ribbon: the translocation of a 4.4 kb sequence deleted from chr19 and inserted into chr16 (Figure 1b). Thus, Ribbon enables understanding of complex variants, and it may also help in the detection of sequencing and sample preparation issues, testing of aligners and variant-callers, and rapid curation of structural variant candidates (Supplementary Note 3). In addition to SAM and BAM files with long, short, or paired-end reads, Ribbon can also load coordinate files from whole genome aligners such as MUMmer. Therefore, Ribbon can be used to test assembly algorithms or inspect the similarity between species. Supplementary Note 4 shows a comparison of gorilla and human genomes using Ribbon, highlighting major structural differences. In conclusion, Ribbon is a powerful interactive web tool for viewing complex genomic alignments.

Script at https://github.com/MariaNattestad/ribbon

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

eFORGE.v1.2

Jit — Fri, 28 Oct 2016 09:06:59 -0500

The eFORGE tool provides a method to view the tissue specific regulatory component of a set of EWAS DMPs. eFORGE analysis takes a set of DMPs, such as those hits above genome-wide significance threshold in an EWAS study, and analyses whether there is enrichment for overlap of putative functional elements compared to matched background DMPs. It assesses enrichment on a per cell type basis, since functional elements are differentially active in different cell types, and hence can expose tissue-specific signals of enrichment for the given test DMP set. This can reveal the sites of action underlying the EWAS signal, and provide confirmation of the validity of the EWAS where a tissue-specific mechanism is known or expected for the phenotype. Conversely unknown tissue involvements can also be revealed.

Address of the bookmark: http://eforge.cs.ucl.ac.uk/eFORGE.v1.2/?documentation

ART: Set of Simulation Tools

Jit — Thu, 03 Nov 2016 08:28:25 -0500

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. VarSim) for evaluating variant calling tools or methods.

Address of the bookmark: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

Minia

Jit — Thu, 08 Dec 2016 05:07:00 -0600

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Download

Minia 2.0.7 Linux 64-bits binaries (Source code) (Legacy codebase)

For the impatient

A typical Minia command line looks like:

./minia -in reads.fa -kmer-size 31 -abundance-min 3 -out output_prefix

Type

./minia

for a quick explanation of the parameters.

For more information, refer to the manual.

KmerGenie can be used to determine the best k-mer size, minimum abundance of correct k-mers, and genome size estimation for your dataset.

Address of the bookmark: http://minia.genouest.org/

GARM:Genome Assembly, Reconciliation and Merging

Jit — Mon, 19 Dec 2016 06:03:02 -0600

The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaffolds from different assemblers using the same or different sequencing technologies. When scaffolds are provided, a process of finding probable compressions or extensions (CE) problems in the assemblies can be per-formed; contigs are joined back into scaffolds after gap recalculation

Address of the bookmark: http://garm-meta-assem.sourceforge.net/

quickmerge: A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Jit — Mon, 19 Dec 2016 10:23:36 -0600

quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBio long reads alone. This is counterintuitive because illumina short reads are not typically considered to cover genomic regions which PacBio long reads cannot. Although we have not evaluated this program for assemblies generated with Oxford nanopore sequences, the program should work with ONP-assemblies too.

Address of the bookmark: https://github.com/mahulchak/quickmerge

PANDASEQ

Shruti Paniwala — Mon, 23 Jan 2017 04:54:32 -0600

PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable region of the 16S gene, or the constant regions around zinc finger binding residues), they can be removed from the sequence during assembly. The final sequence will correct any uncalled bases in the overlapping region using the complementary strand. When mismatches occur in the overlapping region, the base with the better quality score is chosen.
The algorithm is as follows:

1.Find the positions where the forward and reverse primers match best above the threshold and discard the ends of the sequence, including the primer.
2.Pick and overlap to maximise the probability of the forward and reverse reads having come from a single piece of DNA.
3.Identify the masking of the end of the read with the quality score B or # as done by CASAVA and adjust the probabilities in this region.
4.Construct an assembled sequence between the primers and calculate the quality.
5.Check for various constraints, including quality, length, uncalled bases, and user-supplied modules.

http://neufeldserver.uwaterloo.ca/~apmasell/pandaseq_man1.html

Address of the bookmark: http://neufeldserver.uwaterloo.ca/~apmasell/pandaseq_man1.html

Harvest

Jit — Tue, 31 Jan 2017 10:57:56 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

J-Circos

Shruti Paniwala — Fri, 17 Feb 2017 09:06:54 -0600

Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Address of the bookmark: http://www.australianprostatecentre.org/research/software/jcircos

List of popular bioinformatics software/tools

Jitendra Narayan — Tue, 16 Jul 2013 14:30:30 -0500

In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.

Address of the bookmark: http://samtools.sourceforge.net/swlist.shtml