1. Merge re-sequenced FastQ files (cat)
2. Read QC (FastQC)
3. Adapter trimming (fastp)
4. Removal of host reads (Kraken 2; optional)
5. Variant calling
   1. Read alignment (Bowtie 2)
   2. Sort and index alignments (SAMtools)
   3. Primer sequence removal (iVar; amplicon data only)
   4. Duplicate read marking (picard; optional)
   5. Alignment-level QC (picard, SAMtools)
   6. Genome-wide and amplicon coverage QC plots (mosdepth)
   7. Choice of multiple variant calling and consensus sequence generation routes (iVar variants and consensus; default for amplicon data || BCFTools, BEDTools; default for metagenomics data)
      • Variant annotation (SnpEff, SnpSift)
      • Consensus assessment report (QUAST)
      • Lineage analysis (Pangolin)
      • Clade assignment, mutation calling and sequence quality checks (Nextclade)
      • Individual variant screenshots with annotation tracks (ASCIIGenome)
   8. Intersect variants across callers (BCFTools)
6. De novo assembly
   1. Primer trimming (Cutadapt; amplicon data only)
   2. Choice of multiple assembly tools (SPAdes || Unicycler || minia)
      • Blast to reference genome (blastn)
      • Contiguate assembly (ABACAS)
      • Assembly report (PlasmidID)
      • Assembly assessment report (QUAST)
7. Present QC and visualisation for raw read, alignment, assembly and variant calling results (MultiQC)

Reference Number IIT/SRIC/R/DIC/2014/314, DATED 28thNovember, 2014

Temporary Position(s)

i) Junior/ Senior Project Officer (1)
ii) Junior Project Assistant (2)

Consolidated Compensation

i) Rs.16,000/- to Rs.18,000/- p.m. (depending on qualification & experience)
ii) Rs.8,000/- to Rs.10,000/- p.m. (depending on qualification & experience)

Coordinator / PI Dr. Sudip K. Ghosh, Dept of Biotechnology.

Department / Centre / School Dept of Biotechnology

Qualifications & Experience

(i) M. Sc in any branch of Life Sciences with experience in Molecular Biology/Genetics/Biochemistry preferably a Post Graduate diploma in Bioinformatics or two years working experience in bioinformatics (Minimum 60% marks starting from matriculation examination).

(ii) B. Sc. /B.A. /B. Com/Diploma in Management or Computer Science. Knowledge in computer software will be preferred (minimum 50% marks starting from matriculation examination).

More Information

Interested eligible persons may apply on plain paper, giving full bio-data along with attested copies of testimonials to the undersigned on or before 11thDecember, 2014.

Sponsor DBT, NEW DELHI

Last Date 11 Dec 2014

Application Fee Demand Draft for Rs.50/- (Not for female candidates) drawn in favour of IIT Kharagpur payable at Kharagpur

Advertisement: www.iitkgp.ac.in/topfiles/sric_job_details.php?serial=2826

USAGE:

• -query: sequence A in fasta format
• -db: sequence B in fasta format
• -out: output matrix
• -kmer Integer: k>1 (default 32) Use 32 for chromosomes and genomes and 16 for small bacteria
• -diffuse Integer: z>0 (default 4) Use 4 for everything - if using large plant genomes you can try using 1
• -dimension Size of the output matrix and plot. Integer: d>0 (default 1000) Use 1000 for everything that is not full genome size, where 2000 is recommended

Address of the bookmark: https://github.com/estebanpw/chromeister

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

Originally design to map the location of objects in a 10 km map IrishGrid includes:

• native support of the Irish Grid System (see http://www.osi.ie/)
• optimize for speed (there's as less as possible data to conversion)
• customized color functions

https://code.google.com/p/irishgrid/downloads/detail?name=irishgrid.pl

Address of the bookmark: https://code.google.com/p/irishgrid/

What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a high throughput program dealing with lower quality data. Examples include low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data, retrieving low-copy nuclear genes from medium coverage (5x nucDNA) genome skimming.

License: GNU General Public License

Citation:

• Cai, Liming, Hongrui Zhang, and Charles C. Davis. 2022. PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome‐skimming data. Applications in Plant Sciences 10(3): 1–9. https://doi.org/10.1002/aps3.11475

Address of the bookmark: https://github.com/lmcai/PhyloHerb/

1. Remuneration : Rs. 12000/- per month (consolidated)

2. Qualification : M.Sc./M.Tech. Bioinformatics (preference will be given to the candidates with BINC / NET / GATE / Bioinformatics DBT-Traineeship / Studentship and teaching experience)

3. Place of work : Department of Bioinformatics, SVIMS, Tirupati

4. No. of Position : One

Terms and conditions:

1. Candidates are required to submit the Biodata, attested copies of relevant certificates in support of their age, educational qualification, experience etc., before the interview committee, SVIMS University, Tirupati.
2. No TA / DA will be paid for attending the interview.
3. Interim enquiries will not be entertained.
4. The maximum age limit for Teaching Assistant is 34 years as on 8th August, 2015.
5. The tenure of will be further extended subject to performance of the incumbent.

Advertisement: http://svimsbic.org/Teaching_Assistant_B.I._2015.pdf

Key Findings of the Study:

1. Alu Insertion and Tail Loss:
   The researchers discovered an Alu-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.

2. Gene Disruption Mechanism:
   The Alu insertion was found within a regulatory region of the TBXT gene (also known as T or Brachyury), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.

3. Functional Evidence from Model Organisms:
   To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.

4. Evolutionary Implications:
   The findings suggest that small, random genomic changes—such as transposable element insertions—can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like Alu) can drive major evolutionary transitions.

5. Relevance to Human Evolution:
   Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.

Significance of the Study:

This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.