• 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

Script are moved to http://bioinformaticsonline.com/snippets/view/34633/clump-finding-problem-solved-with-perl

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

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

Qualifications : Ph. D.

Desirable : Experience on DNA Markers, plant genome mapping and bioinformatics

No. of Post : 03

Department : Genetics

Salary : Rs. 60,000/-
How to apply

The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room. Applicants are requested to bring all related documents, in original and a set of photocopy, for verification. Date and time of the interview : 25.06.2015 at 10:30 AM.

Click Here for Job Details http://www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=5492&cntnt01returnid=83

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

Applications are invited from individuals who have high motivation to do research for the below mentioned position,

1. Research Associate - 1 No.
in the DBT sponsored project under the supervision of Dr. D. Prabaharan, Principal Investigator, National Facility for Marine Cyanobacteria, Dept. of Marine Biotechnology, Bharathidasan University, Tiruchirappalli-24.

Title of the Project: “Establishment of National Repository for Micro algae & Cyanobacteria” funded by Department of Biotechnology, Govt. of India

Qualification

1. Research Associate – 1 No. Rs. 36,000/38,000/40,000 per month for I, II and III year + 20% HRA

Essential : Doctoral degree in relevant subject from recognized University/ Institutes
Desirable: Research experience in molecular biology and bioinformatics

Interested candidates can send their complete CV in plain paper with a passport size photograph, with details of Marks secured in all subjects from plus two stage (with proof, full postal address, sex, date of birth, community etc., along with additional qualification or experiences and two address of references whom could be contacted (One of whom should be PG teacher/guide). Application should reach the Principal Investigator on or before 30.06.2015 by Email (nfmcbic@yahoo.com)/Registered post/ Speed post, with subject subscribed as “Application for Research Associate /Technical Assistant /Lab attendant”. Qualifying candidates will be short listed and communicated with date of interview. No TA and DA will be given for attending the interview. Addressfor Communication Dr. D. Prabaharan Principal Investigator National Facility for Marine Cyanobacteria Bharathidasan University Tiruchirappalli-620024, Tamil Nadu.

Advertisement: http://www.bdu.ac.in/adv/NFMC_Project_Positions.pdf