BOL: Related items

BioRG

Tue, 04 Aug 2015 20:52:52 -0500

This research group works on problems from the fields of Bioinformatics, Biotechnology, Data Mining, and Information Retrieval. The group's research projects includes Comparative Genomics of Bacterial genomes, Metagenomics, Genomic databases, Pattern Discovery in sequences and structures, micro-array data analysis, prediction of regulatory elements, primer design, probe design, phylogenetic analysis, medical image processing, image analysis, data integration, data mining, information retrieval, knowledge discovery in electronic medical records, and more.

More at http://biorg.cis.fiu.edu/

liftover

Jitendra Narayan — Mon, 08 Feb 2016 15:45:03 -0600

Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly.

More at https://github.com/aaronwolen/liftover

https://www.bioconductor.org/help/workflows/liftOver/

Address of the bookmark: https://github.com/aaronwolen/liftover

Platanus

Jit — Fri, 13 May 2016 05:12:40 -0500

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of
highly heterozygous diploids from massively parallel shotgun sequencing data.

The latest version is 1.2.4.

To cite Platanus, please use the following:

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113. [abstract | full text]

Address of the bookmark: http://platanus.bio.titech.ac.jp/

Samtools Primer !!

Jit — Thu, 23 Jun 2016 07:18:17 -0500

SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.

keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introduction
Revisions

    1.0: May 30, 2013: First public release on biobits.org.
    1.1: July 24, 2013: Updated with Disqus Comments / Feedback section.
    1.2: December 19, 2014: Multiple updates, including:
        Updated to use samtools 1.1 and bcftools 1.2.
        Updated usage for bcftools.

About

SAMtools is a popular open-source tool used in next-generation sequence analysis. This primer provides an introduction to SAMtools, and is geared towards those new to next-generation sequence analysis. The primer is also designed to be self-contained and hands-on, meaning that you only need to install SAMtools, and no other tools, and sample data sets are provided. Terms in bold are also explained in the glossary at the end of the document.

Address of the bookmark: http://biobits.org/samtools_primer.html

Method in Comparative genomics !!

Jit — Wed, 09 Nov 2016 16:29:24 -0600

We present methods for the automatic determination of genome correspondence. The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome. The remaining ambiguities in the gene correspondence revealed recent gene family expansions in regions of rapid genomic change.

We present methods for the identification of protein-coding genes based on their patterns of nucleotide conservation across related species. We observed the pressure to conserve the reading frame of functional proteins and developed a test for gene identification with high sensitivity and specificity. We used this test to revisit the genome of S. cerevisiae, reducing the overall gene count by 500 genes (10% of previously annotated genes) and refining the gene structure of hundreds of genes. We present novel methods for the systematic de novo identification of regulatory motifs. The methods do not rely on previous knowledge of gene function and in that way differ from the current literature on computational motif discovery. Based on the genome-wide conservation patterns of known motifs, we developed three conservation criteria that we used to discover novel motifs. We used an enumeration approach to select strongly conserved motif cores, which we extended and collapsed into a small number of candidate regulatory motifs. These include most previously known regulatory motifs as well as several noteworthy novel motifs. The majority of discovered motifs are enriched in functionally related genes, allowing us to infer a candidate function for novel motifs.

Our results demonstrate the power of comparative genomics to further our understanding of any species. Our methods are validated by the extensive experimental knowledge in yeast, and will be invaluable in the study of complex genomes like that of human.

Address of the bookmark: http://web.mit.edu/manoli/www/publications/Kellis_JCB_04.pdf

MCscan

Bulbul — Thu, 22 Dec 2016 03:53:58 -0600

MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.

More at http://chibba.agtec.uga.edu/duplication/mcscan/

Address of the bookmark: http://chibba.agtec.uga.edu/duplication/mcscan/

SpeedSeq

Jit — Fri, 20 Jan 2017 06:05:43 -0600

A flexible framework for rapid genome analysis and interpretation

C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

Address of the bookmark: https://github.com/hall-lab/speedseq

sockeye

Jit — Fri, 17 Feb 2017 08:51:16 -0600

This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

Salzberg lab

Mon, 15 May 2017 05:14:01 -0500

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

https://salzberg-lab.org/

Software and Tools to detect structure variation with long reads !!

Archana Malhotra — Wed, 15 Mar 2017 14:31:09 -0500

Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs detectable by short-read data.

With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:

Uncover missing heritability linked to structural variation
Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
Resolve structural variation across the complete size spectrum with basepair resolution

Following are the SV tools, which can assist you to achieve your goal.

Sniffles: Structural variation caller using third generation sequencing

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled!

More at https://github.com/fritzsedlazeck/Sniffles

MultiBreak-SV: It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.

More at https://github.com/raphael-group/multibreak-sv

Parliament: A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?

Publication about the algorithm and “…the first long-read characterization of structural variation in a diploid human personal genome…” (HS1011) - “Assessing structural variation in a personal genome—towards a human reference diploid genome”

More at https://sourceforge.net/projects/parliamentsv/

https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf

PBHoney: the structural variation discovery tool

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract

More at https://sourceforge.net/projects/pb-jelly/

SMRT-SV: Structural variant and indel caller for PacBio reads

Structural variant (SV) and indel caller for PacBio reads based on methods from Chaisson et al. 2014.

SMRT-SV provides an official software package for tools described in Chaisson et al. 2014 and adds several key features including the following.

Unified variant calling user interface with built-in cluster compute support
Small indel calling (2-49 bp)
Improved inversion calling (screenInversions)
Quality metric for SV calls based on number of local assemblies supporting each call
Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions
Genotyping of SVs with Illumina paired-end reads from WGS samples

More at https://github.com/EichlerLab/pacbio_variant_caller