BOL: Related items

ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

Neel — Thu, 16 Jan 2020 23:16:02 -0600

ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from the data). By "cohort" we mean samples sequenced with the same enrichment kit with approximately the same depth (ie 1x WGS and 30x WGS better be analysed in separate runs of ClinCNV). Of course it is better if your samples were sequenced within the same sequencing facility.

Address of the bookmark: https://github.com/imgag/ClinCNV

SRF post in NEHU, Shillong

Sat, 25 Jul 2015 20:09:50 -0500

Dept of Biochemistry
North-Eastern Hill University
Umshing, Shillong- 793 022

Applications are invited for the post of Senior Research Fellow- SRF (one) and Junior Research Fellow- JRF (one) to be appointed in a SERB-funded major research project entitled “Biochemical and functional properties of Synechocystis Glutathione S-transferase(s)” sanctioned to Dr. Timir Tripathi, Molecular and Structural Biophysics Laboratory, Department of Biochemistry, NEHU, Shillong.

Essential Qualifications: For both positions M.Sc. or equivalent with a good academic record is a prerequisite.

For Project-SRF, experience in bioinformatics/computational biology is required, which should be evident by publications.

Students waiting for their last semester result can apply for JRF position.

Stipend: As per SERB norms.

Interested students can email their detailed bio-data including mobile number and recent photograph to msb.biochem@gmail.com, latest by 01.08.15. The hard copy is not required at this stage.

The date of interview will be informed after primary scrutiny of the applications. No TA/DA will be paid if called for interview. P.S: Students applied for the same post as per date 01.06.15, need not to apply again as their application will be considered in this advertisement also.

For details of the research work of the PI’s group kindly visit www.ttripathi.webs.com

Dr. Timir Tripathi Principal Investigator DST-SERB Project Department of Biochemistry NEHU, Shillong

Advertisement: www.nehu.ac.in/Advertisements/BiochemPVAdvtTT_200715.pdf

LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data

BioStar — Tue, 18 Feb 2020 03:24:22 -0600

LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

https://github.com/CSB5/lofreq

http://csb5.github.io/lofreq/installation/

https://github.com/CSB5/lofreq/tree/master/dist

Address of the bookmark: http://csb5.github.io/lofreq/

RA Bioinformatics at Alagappa University

Sat, 08 Aug 2015 01:36:35 -0500

RA Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)

Location : Chennai

Last Date : 20 Aug 2015

Hiring Process : Walk - In
Alagappa University - Job Details

RA Bioinformatics Job position in Alagappa University

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

No.of Post: One

Salary : Rs. 11000
How to apply

A walk-in Interview will be held at the Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 004 on 20.08.2015 (Thursday) at 10.30 AM.

Interested candidates are encouraged to send their Curriculum Vitae by email in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview.

Click Here for more http://alagappauniversity.ac.in/files/news_files/Notification.pdf

FiNGS: Filters for Next Generation Sequencing

Neel — Sat, 27 Feb 2021 01:18:35 -0600

Key features

Filters SNVs from any variant caller to remove false positives
Calculates metrics based on BAM files and provides filtering not possible with other tools
Fully user-configurable filtering (including which filters to use and their thresholds)
Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

Bioinformatics Made Easy Search: Bioinformatics tools and run genomic analysis in the cloud

Rahul Nayak — Thu, 20 Aug 2015 02:21:20 -0500

InsideDNA makes hundreds of bioinformatics tools immediately available to run via an easy-to-use web interface and allows an accurate search across all functions, tools and pipelines.

With InsideDNA, you can upload and store your own genomic/genetic datasets in a limitless cloud space, and instantly analyze it with a powerful compute instance, without any tool installation or set up hassle.

More at https://insidedna.me/

Address of the bookmark: https://insidedna.me/

Libraries or management tools for high throughput sequencing data

LEGE — Fri, 04 Oct 2024 02:45:06 -0500

GATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.
These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Among them are (the full is available here: https://gatb.inria.fr/software/):
LRez: C++ Library and toolkit for the barcode-based management and indexation of linked-read datasets.

Variant calling and/or genotyping

DiscoSNP++ and discoSnpRAD: Reference-free small variant discovery (SNPs and indels)
MindTheGap: Detection and assembly of large insertion variants
TakeABreak: reference-free inversion discovery tool
SVJedi: Structural Variant genotyper with long read data
SVJedi-graph: Structural Variant genotyper with long read data using a variation graph

Sequence assembly

MinYS: reference-guided genome assembly in metagenomics data
MTG-link: local assembly tool for linked-read data
Minia: De novo short read assembler
de-novo pipeline: de-novo assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes
Mapsembler2: Targeted assembly (not maintained)

Managing k-mers & indexation

findere: simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure.
- fimpera extends findere adding the abundance information.
kmtricks: modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.
kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
back to sequences: Find sequences (reads, unitigs, genes) related to a set of kmers in large datasets, in a matter of seconds.
Backpack Quotient Filter: k-mer indexing data structure with abundance
short read connector: Detect similar reads from potentially large read set
DSK: Count K-mer in sequences

Pangenome graph manipulation

Pancat: Pangenome Comparison and Analysis Toolkit
GFAGraphs: a Python library to handle pangenome graph files in GFA format.

Comparative metagenomics with k-mers

Simka and SimkaMin: Comparative metagenomics for large-scale datasets
Comparead & Commet: comparison of metagenomic datasets

Species and bacterial strains identification

ORI: software using long nanopore reads to identify bacteria present in a sample at the strain level
StrainFLAIR: STRAIN-level proFiLing using vArIation gRaph

General-purpose sequencing data manipulation

GASSST: long read mapper
Leon: short read compressor (now included in GATB-core)
Bloocoo: short read corrector
BCALM: Construct compacted de Bruijn graphs (unitigs)

Protein Structure

A_Purva: Contact Map Overlap solver
MD-Jeep: Distance Geometry solver
CSA: Comparative Structural Alignment

Workflow

SLICEE: parallel execution of bioinformatics workflows

Comparative Genomics

CASSIS: detection of rearrangement breakpoints
PLAST: intensive bank-to-bank sequence comparison
DRJBreakpointFinder: detection and precise localization of excision sites in proviral segments

JRF Position – International Institute of Information Technology, Hyderabad

Mon, 24 Aug 2015 22:44:46 -0500

International Institute of Information Technology, Hyderabad

Center for Computational Natural Sciences and Bioinformatics

Junior Research Fellowship Position

Applications are invited for one JRF position in the following DAE sponsored project.

Title of the project: Insight into the Structure–Function Relationships of Chemically Modified Nucleic Acids: A Molecular Dynamics Simulations Study.

The above project involves theoretical modelling and simulations on chemically modified nucleic acids to investigate their structures, dynamics and thermodynamic stabilities.

Desired qualification: M.Sc. in Chemistry/ Bioinformatics; GATE/UGC-CSIR NET qualification.

To apply: Send detailed curriculum vitae by e-mail to the following address on or before 31 August 2015: Prof. U. Deva Priyakumar (devalab@iiit.ac.in), CCNSB, IIIT-H, Gachibowli, Hyderabad 500 032.

1mb long DNA with Nanopore technology

Jit — Tue, 19 Dec 2017 18:49:28 -0600

The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

Cancer research database

Neel — Tue, 01 Sep 2015 17:36:31 -0500

Researchers in Andhra Pradesh have developed a database to identify genes that are common in tumours to provide their colleagues with easy access to insights into the genetic alterations in cancer.

The database, hosted at the Sri Venkateswara University (SVU) in Tirupati, will integrate information on cancer genes and markers with experimental data.

The Cancer Gene Markers Database (CGMD) is meant to help scientists better understand tumour genes and markers at a molecular level by combining data with literature on treatment regimen and recent advances in cancer therapy.

The database is free to access, and already includes 309 genes and 206 markers that correspond to 40 different human cancers. Accompanying literature comes from databases such as the United States’ National Center for Biotechnology Information and the Kyoto Encyclopedia of Genes and Genomes. It also includes experimental data from PubMed.

In a paper published last month in Nature Scientific Reports, the researchers from SVU’s department of animal biotechnology, describes the need for a database for different genes and markers along with their molecular characteristics and pathway associations.