BOL: Related items

Understanding PacBio

Jitendra Narayan — Fri, 24 Feb 2017 10:17:36 -0600

This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you get started with your data processing, as well as information for specialized applications.

Training Resources:

Specialized Applications:

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

ABACAS

Surabhi Chaudhary — Thu, 16 Feb 2017 12:15:55 -0600

ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule.

Address of the bookmark: http://abacas.sourceforge.net/Manual.html#9._Colour_code

FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads

Jit — Mon, 27 Feb 2017 09:49:45 -0600

FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Address of the bookmark: http://kakitone.github.io/finishingTool/

CLgenomics

Radha Agarkar — Fri, 03 Mar 2017 09:57:28 -0600

CLgenomics is a standalone desktop software specifically designed for bacterial genome analysis. This program has a powerful multi-genome browser, which enables rapid and responsive exploration of bacterial genomes.

To use CLgenomics, individual genome data (genome sequences + annotation details) are compiled and saved in a specially formatted file called CLG (ChunLab Genomics). Each CLG file corresponds with one bacterial genome. If multiple genomes are being considered and compared, multiple CLG files are needed. ChunLab offers >40,000 CLG files of publicly available Bacterial and Archaeal genomes.

Address of the bookmark: https://chunlab.wordpress.com/clgenomics-software/

SSPACE

Jit — Fri, 05 May 2017 05:42:15 -0500

SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format.

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

SeqMule: Automated human exome/genome variants detection

Abhimanyu Singh — Tue, 07 Mar 2017 10:12:36 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

UpSetR Shiny App!

Jit — Fri, 14 Apr 2017 06:19:54 -0500

UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

To begin, input your data using one of the three input styles.

"File" takes a correctly formatted.csv file.
"List" takes up to 6 different lists that contain unique elements, similar to that used in the web applications BioVenn (Hulsen et al., 2008) and jvenn (Bardou et al., 2014)
"Expression" takes the input used by the venneuler R package (Wilkinson, 2015)

Address of the bookmark: https://gehlenborglab.shinyapps.io/upsetr/

DIYA: a bacterial annotation pipeline for any genomics lab

Jit — Fri, 30 Jun 2017 08:48:26 -0500

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

http://gmod.org/wiki/Diya

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

CLA: Contig-Layout-Authenticator

Jit — Fri, 05 May 2017 05:58:36 -0500

To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

Script https://sourceforge.net/projects/c-l-authenticator/files/

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155459

Sr.Bioinformatics Analyst (NGS) at Ocimum

Fri, 17 Nov 2017 07:50:44 -0600

JOB FUNCTIONBio Tech/R&D/Scientist
INDUSTRYBiotechnology/Pharmaceutical/Medicine
SPECIALIZATIONBasic Research,Bio-Statistician,Clinical Research
QUALIFICATION
Any Post Graduate
BA (Arts), B.Com. (Commerce), BE/ B.Tech (Engineering), B.Pharm. (Pharmacy), B.Sc. (Science), BL/LLB, BDS (Dental Surgery), B.Ed. (Education), BHM (Hotel Management), BBA/ BBM/ BBS, B.Arch. (Architecture), BCA (Computer Application), Diploma-Other Diploma, B.Plan. (Planning), BGL, B.V.Sc. (Veterinary Science), Other School/ Graduation, BHMS (Homeopathy), BAMS (Ayurveda)
Job Description

1. Must have basic understanding of molecular biology and Genomics.
2. Experience in application development or must have expertise in programming using either of Perl/Python.
3. Experience in statistical programming using R/Bioconductor/Matlab.
4. Strong concept in statistical and mathematical modelling.
5. Experience in designing and developing the bioinformatics pipeline.
6. Must have minimum 2+ years of hands on experience in NSG data analysis such as RNA-Seq,Exome-Seq ,Chip-Seq and downstream analysis.
7. Knowledge in WGS ,WES, Targeted re-sequencing,GWAS and population genomics will be preferred.
8. Must have experience working on opensource software/Framework and commercial software for NGS data analysis and reporting.
9. Should be aware of handling big data and guiding team members on multiple projects simultaneously.
10. Should have experience coordinating with different groups of clinical research scientist for various project requirements.
11. Ability to work as team as well as independently with minimal support.

More at http://www3.ocimumbio.com/