BOL: Related items

Bookmarks Biostatistics materials and books

Jit — Tue, 08 Nov 2016 07:42:42 -0600

Biostatistics did not spring fully formed from the brow of R. A. Fisher, but evolved over many years. This process is continuing, although it may not be obvious from the outside. It has been ten years since the first edition of this book appeared (and rather longer since it was begun). Over this time, new areas of biostatistics have been developed and emphases and interpretations have changed

Please bookmarks your favourate biostatistics books in commend sectons ...

Address of the bookmark: http://www.cos.ufrj.br/~bioestatistica/livros/Introduction%20to%20Biostatistics.pdf

Research Assistant Bioinformatics recruitment in National Institute Of Cancer Prevention & Research (ICMR) on Contract basis

Tue, 15 Nov 2016 17:15:48 -0600

National Institute Of Cancer Prevention & Research - ICMR

Research Assistant Bioinformatics recruitment in National Institute Of Cancer Prevention & Research (ICMR) on Contract basis
Project entitled: “Next generation EGFR inhibitor identification using ligand based QSAR technique”

Essential: M.Sc. in Bioinformatics or related field. Desirable: Experience in QSAR and structure based drug designing.
Age: 28 years
No.of Post: 1

Pay Scale : Rs.27000

Application format is attached and should be sent by post to Dr. Subhash M Agarwal, Scientist D, Division of Bioinformatics, National Institute of Cancer Prevention & Research (ICMR), Plot No. I-7, Sector-39, Noida 201301 (U.P).

More at http://www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf

Maq: Mapping and Assembly with Quality

Jit — Tue, 22 Nov 2016 04:51:39 -0600

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/. Maq is previously known as mapass2.

Run Maq Now

Follow these steps to try Maq. All you need is a reference sequence file in the FASTA format.

Prepare a reference sequence (ref.fasta). Better a bacterial genome.
Download maq, maq-data and maqview at the download page.
Copy maq, maq.pl and maq_eval.pl to the $PATH or to the same directory.
Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go:
```
maq.pl demo ref.fasta calib-30.dat
```
where calib-30.dat is contained in maq-data.

View the alignment:

cd maqdemo/easyrun;
maqindex -i -c consensus.cns all.map;
maqview -c consensus.cns all.map

Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.

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

HGA

Jit — Tue, 29 Nov 2016 07:25:53 -0600

HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler (Velvet or SPAdes in this version) and using a given kmer size. 3. Merging all the assemblies of the partition. 4. Combining all the assemblies of the partition (using velvet with kmer value of 31). 5. Finaly, re-assembling the whole dataset with the merged contigs or the combined contigs, using a given kmer size.

https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

Address of the bookmark: https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA

Scripts

Jit — Wed, 30 Nov 2016 10:35:15 -0600

Useful script for NGS analysis.

Address of the bookmark: http://augustus.gobics.de/binaries/scripts/

e-RGA: enhanced Reference Guided Assembly of Complex Genomes

Jit — Mon, 19 Dec 2016 05:56:14 -0600

Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on top of this list. Despite efforts to design tools able to assemble, de novo, an organism sequenced with short reads, the results are still far from those achievable with long reads. In this paper, we propose a novel method that aims to improve de novo assembly in the presence of a closely related reference. The idea is to combine de novo and reference-guided assembly in order to obtain enhanced results.

Address of the bookmark: http://journal.embnet.org/index.php/embnetjournal/article/view/208

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

CISA: Contig Integrator for Sequence Assembly

Neel — Thu, 15 Dec 2016 05:42:21 -0600

A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. However, few efforts have been pursued to take advantage of multiple assemblies to yield an assembly of high accuracy. In this study, we employ various state-of-the-art assemblers to generate different sets of contigs for bacterial genomes. A tool, named CISA, has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on the local machine. The source code of CISA and examples of its use are available at http://sb.nhri.org.tw/CISA/.

Address of the bookmark: http://sb.nhri.org.tw/CISA/en/CISA

Gene Synteny Database

Jit — Fri, 16 Dec 2016 11:09:39 -0600

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.

Availability: Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus

Contact: rf.sne.eigoloib@crh

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/

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