BOL: Related items

deepTools

Martin Jones — Sat, 08 Nov 2014 15:02:08 -0600

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.

Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full

Source Code and Wiki: https://github.com/fidelram/deepTools/wiki

Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows

Vital-IT

Abhi — Thu, 18 Dec 2014 10:46:59 -0600

Vital-IT is a bioinformatics competence center that supports and collaborates with life scientists in Switzerland and beyond. The multi-disciplinary team provides expertise, training and maintains a high-performance computing (HPC) and storage infrastructure, so as to help develop, maintain and extend life science and medical research (activities).

Address of the bookmark: http://www.vital-it.ch/

LASTZ

Abhi — Mon, 18 Apr 2016 04:41:55 -0500

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

More at http://www.bx.psu.edu/~rsharris/lastz/

Thesis: http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

Address of the bookmark: http://www.bx.psu.edu/~rsharris/lastz/

Ensembl comparative genomics resources

Jitendra Narayan — Sun, 28 Feb 2016 17:10:20 -0600

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

RATT

Jitendra Narayan — Sun, 07 Feb 2016 16:09:40 -0600

RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmodium chabaudi onto P. berghei, between different Leishmania species or Salmonella enterica onto other Salmonella serotypes. RATT is able to transfer any entries present on a reference sequence, such as the systematic id or an annotator's notes; such information would be lost in a de novo annotation.

More at http://ratt.sourceforge.net/

Address of the bookmark: http://ratt.sourceforge.net/

Efficient genome searching with Biostrings and the BSgenome data package

Aasha — Mon, 07 Mar 2016 05:18:06 -0600

Address of the bookmark: https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

A5-miseq

Jit — Thu, 18 Aug 2016 04:05:23 -0500

_A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_.

Point to note:

There are many situations where A5-miseq is not the right tool for the job. In order to produce accurate results, A5-miseq requires Illumina data with certain characteristics. A5-miseq will likely not work well with Illumina reads shorter than around 80nt, or reads where the base qualities are low in all or most reads before 60nt. A5-miseq assumes it is assembling homozygous haploid genomes. Use a different assembler for metagenomes and heterozygous diploid or polyploid organisms. Use a different assembler if a tool like FastQC reports your data quality is dubious. You have been warned! Datasets consisting solely of unpaired reads are not currently supported.

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

VAGUE:Velvet Assembler Graphical Front End

Jit — Fri, 24 Feb 2017 08:56:49 -0600

VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginners to use, but VAGUE makes it clear and simple

More at http://www.vicbioinformatics.com/software.vague.shtml

Address of the bookmark: http://www.vicbioinformatics.com/software.vague.shtml

RepeatModeler

Jit — Thu, 18 Aug 2016 09:57:15 -0500

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

Address of the bookmark: http://www.repeatmasker.org/RepeatModeler.html