BOL: Related items

BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,

Jit — Wed, 23 May 2018 06:54:32 -0500

BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error.

Here is how I use the blasr to align PacBio reads to the contigs (target.fasta). The “target.fasta.sa” is the suffix array from “target.fasta” generated by sawriter.

blasr query.fa ./target.fasta -sa ./target.fasta.sa -bestn 40 -maxScore -500 -m 4 -nproc 24 -out target.m4 -maxLCPLength 15

the output format option “-m 4″ generate the alignment coordinate. Not fully documented, but I can explain that to you.

I use a 24 cores / 48G ram server for the alignment. It took about 2 to 3 hours aligning 3G PacBio Reads to 10^6 sequences of short read contigs with a mean 3.5kbp length.

Address of the bookmark: http://bix.ucsd.edu/projects/blasr/

Software developed in pevsner lab

Robert M Willioms — Mon, 06 Oct 2014 12:41:26 -0500

DRAGON: Database Referencing of Array Genes Online

SNOMAD: Standardization and Normalization of Microarray Data

SNPduo: SNP Analysis Between Two Individuals

SNPtrio: Analyzing and Visualizing and Inheritance Patterns in Trios

SNPscan: Data Analysis and Visualization of SNP Data

pediSNP: Analyze SNP Data From a Pedigree of Two Generations

kcoeff: Calculate Cotterman Coefficients of SNP Genotype Data

triPOD: Detects chromosomal abnormalities in parent-child trio-based microarray data

Address of the bookmark: http://pevsnerlab.kennedykrieger.org/php/?q=software

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data

Rahul Nayak — Tue, 03 Jul 2018 04:14:52 -0500

ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm also detects base substitutions in transcript sequences corresponding to sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are reported as splice graphs in dot output format.

Address of the bookmark: https://github.com/bcgsc/ChopStitch

Research Fellows at CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh

Tue, 19 May 2015 07:17:32 -0500

CSIR - Institute of Himalayan Bioresource Technology 2 vacancies of Project Fellow

Name of the Post: Project Fellow

No. of the Post: 02 Two

Salary: Rs. 12000/- per month or Rs. 14000/- per month

Age Limit: Max. 28 years as on 10.06.2015 and relaxation as per rules

Required Job Profile:

Candidate must possess first class B.Tech. in bioinformatics or computational biology OR M.Sc. in bioinformatics or computational biology with fifty five percent marks OR M.Tech. in bioinformatics or computational biology with fifty five percent marks.

How to apply:

Eligible and interested candidates should need to appear for walk-in interview on 10.06.2015 at 9:00 am at the above mentioned address.

Refer to http://www.ihbt.res.in/recruit/AdvtNo7_2015.pdf

PureCN: copy number calling and SNV classification using targeted short read sequencing

Jit — Thu, 09 Aug 2018 04:09:37 -0500

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Author: Markus Riester [aut, cre], Angad P. Singh [aut]

Maintainer: Markus Riester

Citation (from within R, enter citation("PureCN")):

Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, 13. doi: 10.1186/s13029-016-0060-z.

Address of the bookmark: http://bioconductor.org/packages/release/bioc/html/PureCN.html

Big genomic data on Google Cloud Platform

Fri, 17 Oct 2014 02:16:00 -0500

As the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define a standard API for working with big genomic data sets in the cloud. Building on Google Cloud Platform, we show how to store, process, explore and share genomic data using technologies like BigQuery, AppEngine MapReduce, R and more.

LoRMA: A tool for correcting sequencing errors in long reads

Abhimanyu Singh — Thu, 06 Sep 2018 16:21:01 -0500

An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher.

conda install -c atgc-montpellier lorma

Address of the bookmark: https://gite.lirmm.fr/lorma/lorma-releases/wikis/home

CLUSTER INNOVATION CENTER @ UNIVERSITY OF DELHI

Wed, 22 Oct 2014 10:39:49 -0500

Applications for Pre-selection of candidates under ‘Institutions Mode’ for DST-ISPIRE Faculty in Computational Biology/ Systems Biology/ Bioinformatics

Applications are invited for pre-selection of candidates for Ministry of Science and Technology, Department of Science and Technology INSPIRE Faculty Scheme: a component of “Assured Opportunity for Research Career (AORC)” under INSPIRE in the area of computational Biology/Systems Biology/Bioinformatics.

Candidates having done their B.Tech/B.E. and or M.Sc./M.Tech in Computer Science or Biotechnology and Ph.D. in Systems/ Computational Biology or Bioinformatics may apply in the following format prescribed by DST to the Director, Cluster Innovation Center, University Stadium, GC Narang Marg, University of Delhi, Delhi -11107. Detials of other qualification, age limits etc., please visit www.inspire-dst.gov.in.

Application on the prescribed format may be submitted by email to director@cic.du.ac.in before October 25, 2014. Selected candidates shall be called for an interview. The date, time and venue of the interview shall be informed by email/telephone. For more information about Cluster Innovation Center, please visit https://ducic.ac.in.

VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules

Rahul Nayak — Thu, 04 Oct 2018 16:30:44 -0500

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem.

Address of the bookmark: https://github.com/broadinstitute/VariantBam

IPython: Interactive notebooks

Rahul Nayak — Fri, 07 Nov 2014 12:07:02 -0600

The IPython Notebook is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document.

These notebooks are normal files that can be shared with colleagues, converted to other formats such as HTML or PDF, etc. You can share any publicly available notebook by using the IPython Notebook Viewer service which will render it as a static web page. This makes it easy to give your colleagues a document they can read immediately without having to install anything.

To learn more about using the IPython Notebook, you can visit our example collection, and you can read the documentation for all the details on how to use and configure the system. The Notebook Gallery showcases many interesting notebooks covering a variety of topics, from basic programming to advanced scientific computing.

More http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261

http://ipython.org/ipython-doc/1/interactive/notebook.html

Reference http://ipython.org/notebook.html