Project planning

Project planning

Purpose

The main objective of the paper is to reproduce the work on the paper “ Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT”. This includes, to analyse functionally annotate genome and mRNA transcripts to find differential expression in Leptospirillum ferriphilum in order to improve biomining process. Analysis of genome is to understand atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. In the paper mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). This is to study the adaptations to the growth by enhanced production of reducing power, reduced carbon dioxide fixation and heavy metal resistance.

Workflow

Basic Analysis

The below tasks come under basic analysis:

1. Raw data collection and understanding it.
2. Pre processing and Quality Controls.
3. Sequencing PacBio reads
4. Assembling the genome using Canu. (~ 11,5 h (2 cores))
5. Assembly quality assessment is done using Quast from the fasta sequence from the genome assembly (< 15 min (1 core))
6. Synteny comparison with a closely related genome using MUMmerplot (on the fasta sequence from Quast analysis and assembly of closely related organism)(< 5 min (1 core))
7. Structural and functional annotation using eggNOGmapper online using precomputed eggNOG-based orthology entries and also using Prokka (~ 1 h (HMM algorithm) for eggNOGmapper and (< 5 min (2 cores)) for prokka)
8. Reads preprocessing and quality check of RNA reads will be done using Trimmomatic on the Illumina data (~ 15 min per file (2 cores))
9. Reads alignment using BWA (~ 5 h (2 cores))
10. Mapping and counting RNA-seq reads, and analysing differential expression using Htseq (~ 8 h)

Extra analyses:

The below tasks come under extra analysis:

1. Comparative genomics: comparison of genes in common with 1 or more species using MUMmerplot (< 5 min (1 core) * number of species)
2. Identification of other sequences within the genome (promoters, repeats, mobile elements, …)