BOL: Related items

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Jit — Wed, 14 Nov 2018 04:50:27 -0600

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8.

https://academic.oup.com/bioinformatics/article/31/10/1674/177884

Address of the bookmark: https://github.com/voutcn/megahit

Entrez Direct: E-utilities on the UNIX Command Line

Anjana — Wed, 19 Oct 2016 08:06:24 -0500

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK179288/

PLINK2

Jit — Thu, 27 Oct 2016 11:24:45 -0500

This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others. (What's new?) (Credits.) (Methods paper.)

Address of the bookmark: https://www.cog-genomics.org/plink2/

SDA: Long-read sequence and assembly of segmental duplications

Jit — Tue, 05 Mar 2019 10:00:57 -0600

Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs.

https://github.com/mvollger/SDA

Address of the bookmark: https://www.nature.com/articles/s41592-018-0236-3

StringTie Transcript assembly and quantification for RNA-Seq

Jit — Tue, 09 Jun 2020 05:21:11 -0500

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only alignments of short reads that can also be used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).

Address of the bookmark: https://ccb.jhu.edu/software/stringtie/

Information Officer at IIAR, Gujarat

Fri, 04 Nov 2016 05:19:13 -0500

Walk in interview at 10.30 am on Nov 11th, 2016 for the following position at Distributed Information Sub-Centre (DISC) established by Dept. Of Biotechnology, Govt. of India at Indian Institute of Advanced Research, Gandhinagar, Gujarat

Position (scale), qualifications and experience

1. Information Officer (Rs 8000-275-13500): one post
Qualifications and experience: MCA, Post-Graduate in any field of biosciences, bioinformatics with at least two years of experience in working in a bioinformatics setup and good knowledge of linux operating system and computer networking.

General terms and conditions:
1. The above engagements is presently till March 31st, 2017. However on extension of project grant and satisfactory performance of the candidate, your services can be extended beyond March 31st, 2017 based on the terms and conditions of extension of project grant.

2. It is not an appointment with the institute and will not confer any right to the incumbent to any claim implicit or explicit on any position.

3.No TA/DA will be paid for attending the interview. Outstation candidates have to make their own arrangement for their stay.

4.Candidates, appearing in the walk-in interview are requested to bring the hard copy of application addressed to Dr. Anju Pappachan with latest photograph, CV mentioning qualifications, work experience and name of two referees and one page write up as to why you would like to join the project.

Address:
Dr. Anju Pappachan
Indian Institute of Advanced Research (IIAR),
University and Institute of Advanced Research,
The Puri Foundation for Education in India,
Koba Institutional Area,
Gandhinagar- 382 007, Gujarat, India. Contact no. 079-30514152
e-mail- anju@iiar.res.in

MEC: Contig Misassembly Correction

BioStar — Tue, 04 Feb 2020 23:40:49 -0600

MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the statistical analysis of GC-contents. We apply MEC to four real contig datasets, and carry out experiments to analyze the influence of MEC on scaffolding results, which shows that MEC can reduce misassemblies effectively and result in quantitative improvements in scaffolding quality. MEC is publicly available for download at https://github.com/bioinfomaticsCSU/MEC.

Address of the bookmark: https://github.com/bioinfomaticsCSU/MEC

Junior Research Fellow at Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram

Mon, 07 Nov 2016 10:27:06 -0600

Adv. # 22/ 2016
Applications are invited from suitable candidates for one position of Junior Research Fellow in a DST funded bioinformatics research project entitled "Major gene influxes in microbial genome evolution" in the Laboratory of Dr. Shijulal Nelson-Sathi at Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram.

ESSENTIAL QUALIFICATIONS:
We are looking for a motivated candidate with keen interest in bioinformatics and microbial genome evolution. The candidate must have a Master’s Degree in Bioinformatics, Computational Biology, Computer Science, Microbiology, Biology or a related field with good academic record.

DESIRABLE QUALIFICATIONS
Hands on research experience on handling next generation sequencing data and phylogenetic reconstruction methods. Excellent programming skills (Perl/Python/Java/Php) and experience in working on Unix/Linux platform is preferred. Furthermore; good knowledge is required in statistics (R/Matlab) and the application of bioinformatics analysis tools.

AGE:
Below 28 years as on 15th November, 2016.

EMOLUMENTS:
Rs. 25,000 + 20% HRA for NET/GATE qualified and Post Graduate in Professional Degree course qualified candidates and
Rs. 12,000/- + 20% HRA for others.

DURATION:
Initial appointment will be given for one year and further extension will be based on the performance till termination of the project.
Only those fulfilling the above criteria need apply and will be called for interview. In the event of more than 10 candidates being short-listed by screening the applications, a written test will be conducted before the selection interview and only those who are successful in the written test will be interviewed. No TA/ DA will be given for appearing in the interview.

Suitably qualified candidates may send applications in the prescribed format (Download here) with a photograph, a copy of full resume indicating the percentage of Marks obtained and attested photocopies of credentials & experience to reach the undersigned on or before 15th November, 2016. Envelopes must be superscripted with abbreviated title of the project, advertisement number and job title. Selection to the position will not entitle the candidate to any future positions at RGCB (permanent or otherwise). As with all project positions at RGCB, the position will be co terminus with end of the project.

SvABA: Structural variation and indel detection by local assembly

Jit — Tue, 10 Mar 2020 07:52:15 -0500

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

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