Oskar Lindsjö's repositories
AMB_MAG_Summer_2018
MAG analysis for AMB group, GATC sequencing summer 2018
BITMaB-workshop
Workshop tutorials for the 2017 Benthic Invertebrates, Metagenomics, and Bioinformatics Workshop in Corpus Christi, Tx (January 9-13, 2017)
campylobacter_analysis
Scripts for analysis of Campylobacter from Illumina WGS sequencing
dada2_studio
An R docker with DADA2 preinstalled. Can be run as a Rstudio server.
e_hirae_analysis
Analysis of E.Hirae WGS sequencing data
good-enough-practices-in-scientific-computing
Minimalist alternatives to "best practices" paper
gotree
Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.
hack17-tutorial
Nextflow basic tutorial for newbie users
hello-world
Learning Git... Way to late but still
InSilicoSeq
:rocket: A sequencing simulator
MASH_Phylogeny
Testing building a phylogeny based on Mash distance as in https://www.biorxiv.org/content/10.1101/119420v1.full.pdf
Microbial-community-adaptability-to-altered-temperature-conditions-influences-the-prospect-for-optim
The operating temperature strongly affects biogas yield, process stability and prospect for process optimization. Yet, many questions remains on how changed temperature influences on microbial communities and how to optimally manage the process in association to such changes. A long-term anaerobic digestion experiment was conducted to determine temperature-related questions raised by operative full-scale biogas plants and to evaluate optimization potentials and links to microbial community structure and responses. Four digesters fed household and slaughterhouse waste were operated in sets of two, at 37°C or 52°C, followed by a gradual increase or decrease in temperature in one digester in each set. Stability and flexibility of the digesters were then assessed by step-wise increases in organic loading rate (OLR) from 3 to 7 g VS/L/day, concurrently with decreased hydraulic retention time from 33-40 days to 14-17 days. The digester that had altered from thermophilic to mesophilic conditions failed at 6 g VS/L/day, whereas the digesters with constant temperature and the mesophilic-to-thermophilic digester remained stable at all OLR investigated. Amplicon sequencing showed divergent grouping of the mesophilic communities, whereas the thermophilic communities were nearly identical after the temperature change. Both biological and chemical parameters indicated that lagging in resilience of the acetate and propionate-degrading populations inherited from the community shaped by the initial operation at thermophilic conditions caused the thermophilic-to-mesophilic process less resistant to stress and counteracted process optimization. Overall, these results are valuable in the development of guidelines for process monitoring and strategies during changed temperature conditions with the prospect to optimize performances.
Qiime16sTutorial
A tutorial on up-to-date methods of 16S analysis with QIIME
sangeranalyseR
functions to analyse sanger sequencing reads in R
tutorials
:notebook_with_decorative_cover: Various bioinformatics tutorials
tutorials-1
Tutorials for basics bioinformatics courses
VAPiD_docker
A docker for VAPiD