BOL: Related items

nQuire: A statistical framework for ploidy estimation using NGS short-read data

Jit — Thu, 31 Jan 2019 05:12:19 -0600

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases are segregating.

For more background see also the publication at BMC Bioinformatics.

https://github.com/clwgg/nQuire

Address of the bookmark: https://github.com/clwgg/nQuire

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

Walk-in-interview for SRF, JRF posts at NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY New Delhi-110012

Thu, 10 Sep 2015 15:58:55 -0500

NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY New Delhi-110012

Eligible candidates may appear in Walk-in-interview for the positions of Senior Research Fellow in ICAR funded projects as follows

ICAR Network Project on Transgenics in Crops- Amelioration of cold induced sweetening in potato.

PI: Dr Debasis Pattanayak

SRF

Rs.25000/‐+ 30% HRA

September 29, 2015

Essential: Master’s Degree in Bioinformatics /Biotechnology/ Biochemistry/ life sciences with four years Bachelor’s Degree (or) Master’s Degree in Bioinformatics /Biotechnology/Biochemistry/ life sciences with NET qualification. .

Desirable: Experience in Bioinformatics and programming.

Age Limit: 35 years max. (5 years relaxation for SC/ST/OBC and woman candidates as per ICAR rules).

The post is purely temporary in nature and is co-terminus with the project. The interview will be held on September 29, 2015 at 10 AM at NRCPB, LBS Building, Pusa Campus, and New Delhi-110012. The candidates must bring four copies of biodata, original certificates, attested photocopies of each of the certificates and an attested copy of recent passport size photograph.

No TA/DA would be given for the appearance in interview. Only the candidates having essential qualifications would be entertained for the interviews

http://www.nrcpb.org/sites/default/files/NPTC%20walk%20in%20interview%20September%202015%20for%20NRCPB%20webpage%20D%20%20%20Pattanayak.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/

Guest Faculty Job vacancies in Pondicherry University

Tue, 22 Sep 2015 23:50:16 -0500

Guest Faculty Job vacancies in Pondicherry University
Qualification : M.Phil. / M.Tech. / M.Sc. in Computer Science / Master of Computer Applications with a minimum of 55% of marks. Candidates with Ph.D. degree and NET/SLET qualification will be given preference as per UGC norms.

Desirable : Research or teaching experience in Bioinformatics and Computational Biology.
Honorarium : Rs. 1,000/- per lecture (subject to a maximum of 25,000/- per month)
How to apply

Interested eligible candidates may attend the 'walk-in' interview along with all original certificates and testimonials with a copy of their bio-data. Walk-in-interview will be held on 28.09.2015 (Monday), 03:00 P.M. at the office of the Dean, School of Life Sciences, Science Block — I, Pondicherry University, Puducherry — 605 014. Candidates reporting after 03:00 P.M. will not be entertained.

More at http://www.pondiuni.edu.in/news/walk-interview-guest-faculty-centre-bioinformatics

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 Faculty at University of Pune

Fri, 13 Nov 2015 03:06:00 -0600

SAVITRIBAI PHULE PUNE UNIVERSITY
(Formerly University of Pune)
(APPOINTMENT OF TEACHING POSTS)

Accompaniment to the Advertisement No. 52 dated 10.11.2015 for various Teaching Positions purely on contract basis for a maximum period of five years in the various Departments/Centre of the University.

Last date for receipt of application in the University Office is 04.12.2015.

Associate Professor

Environmental Science

Institute of Bioinformatics & Biotechnology (IBB)

Microbiology

Assistant Professor

Biotechnology

Institute of Bioinformatics & Biotechnology (IBB)

Microbiology

More Info : http://collegecirculars.unipune.ac.in/sites/documents/Job%20Openings/advt-no-52-dt-10-11-2015-contract-positions.pdf

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

Postdoctoral positions are available at the Faryabi Lab

Sun, 11 Oct 2015 03:36:18 -0500

Postdoctoral positions are available at the Faryabi Lab located in the Department of Pathology and the Center for Personalized Diagnostics at the University of Pennsylvania.

A qualified candidate will be strongly motivated individual with following qualifications: a Ph.D. in computational sciences, engineering, physics, bioinformatics, or related field. Ability to program in Python/Perl and R in Unix environment, knowledge of C++, Java, and SQL is a plus. Demonstrated applied bioinformatics/computational proficiency as evidenced by relevant publications in peer-reviewed journals. Experience with cancer genomics is a plus.

The primary research focus of the Faryabi Lab is on developing novel computational methods to study mechanisms involved in genome instability and elucidate their roles in tumorigenesis. In addition the position provides collaborative opportunities with both basic and translational scientists across the Perelman School of Medicine, one of the top 5 medical research universities in the nation.
. a Ph.D. degree in either physical or computational sciences
. solid programming skills ( Python/Perl, Java, C/C++, R, SQL)
. computational genomics experience ( high throughput sequence analysis)
. excellent spoken and written communication and interaction skills
. publications in English in relevant areas of research in peer-reviewed journals.
. Previous experience or interest in data visualization design is a plus.

More at
University of Pennsylvania
Pathology and Laboratory Medicine
Robert B. Faryabi
faryabiPenn@gmail.com
http://faryabib.github.io/
How To Apply: email CV and contacts of 3 references to faryabiPenn@gmail.com

Qualimap2: Evaluating next generation sequencing alignment data

Jit — Tue, 11 Sep 2018 04:44:29 -0500

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Supported types of experiments include:

Whole-genome sequencing
Whole-exome sequencing
RNA-seq (speical mode available)
ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/