BOL: Related items

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

SGA: String Graph Assembler

Jit — Thu, 08 Dec 2016 05:08:59 -0600

SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

More at

https://github.com/jts/sga

SGA dependencies:
-google sparse hash library (http://code.google.com/p/google-sparsehash/)
-the bamtools library (https://github.com/pezmaster31/bamtools)
-zlib (http://www.zlib.net/)
-(optional but suggested) the jemalloc memory allocator (http://www.canonware.com/jemalloc/download.html)

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

MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs

Jit — Mon, 19 Dec 2016 09:42:15 -0600

MeGAMerge

MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)

Description

MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any length in Multi-FASTA format to produce an improved contig set based on OLC based assembly. All overlap parameters (Minimum Overlap Length, Identity, etc) are user-declarable at runtime. It is written to run on Linux.

Requirements:

You will need to have the following tools installed and in $PATH, or added to $binpath in the tool:

Newbler (specifically runAssembly)
Minimus2 (part of AMOS, also requires MUMmer)

Address of the bookmark: https://github.com/LANL-Bioinformatics/MeGAMerge

Jvarkit : Java utilities for Bioinformatics

Jit — Fri, 08 Jun 2018 09:31:55 -0500

Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

Address of the bookmark: http://lindenb.github.io/jvarkit/

MAKER

Jitendra Narayan — Sun, 07 Feb 2016 15:59:24 -0600

MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

More at http://www.yandell-lab.org/software/maker.html

Address of the bookmark: http://www.yandell-lab.org/software/maker.html

Bioinformatics tools and software

Jit — Tue, 05 Jul 2016 10:02:26 -0500

USEARCH >
Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >
Multiple sequence alignment. Faster and more accurate than CLUSTALW.

UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. UCHIME >
Chimeric sequence detection. PILER >
De novo genome repeat finder. PILER-CR >
Detection of CRISPR repeats in bacterial genomes. QSCORE >
Compare two multiple alignments for benchmarking. PALS >
Whole-genome alignment. PREFAB >
Protein Reference Alignment Database. MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.

Address of the bookmark: http://drive5.com/software.html

MEGAN6

Neel — Mon, 25 Jul 2016 05:45:22 -0500

Microbiome analysis using a single application

MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.

Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA
Functional analysis using InterPro2GO, SEED, eggNOG or KEGG
Bar charts, word clouds, Voronoi tree maps and many other charts
PCoA, clustering and networks
Supports metadata
MEGAN parses many different types of input

Why use MEGAN6?

The software is:

Easy to use. MEGAN6 is a single application and all features are available through menus, toolbars and graphics. No scripting skills required.
Powerful. MEGAN6 allows you to work with hundreds of samples containing hundreds of millions of sequencing reads. Blast-like analysis can be performed using DIAMOND.
Comprehensive. MEGAN6 offers a large range of analysis tools, and is under active development.

Address of the bookmark: https://ab.inf.uni-tuebingen.de/software/megan6

EXCAVATOR2tool

Bulbul — Wed, 30 Nov 2016 04:09:19 -0600

EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads. Specifically, it improves the precision of calling CNVs overlapping targeted exons from WES data and enlarges the spectrum of detectable CNVs to off-target events.
EXCAVATOR2 can be effectively employed for the identification of CNVs in small as well as large-scale re-sequencing population and cancer studies. Lastly, it’s of particular interest that all WES experiments can be re-analysed using our method with the beneficial effect to identify novelCNVs in extra-exonic regions by having the full-genome CN profile.

Address of the bookmark: https://sourceforge.net/projects/excavator2tool/

fqtools

Jit — Thu, 08 Dec 2016 09:31:12 -0600

fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are supported. See below for a full list of the subcommands available and a brief description of their purpose. Most of the individual subcommands will take either a single file or a pair of files as input. If no input file is specified, fqtools will attempt to read data from stdin. In this case, it is advisabe to specify the format of the data provided. For subcommands that generate FASTQ data, either a single file or a pair of files will be generated. If no -o argument is provided, single files will be writted to stdout.

Address of the bookmark: https://github.com/alastair-droop/fqtools

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