Tutorial: Bioinformatics For Metagenomic Analyses
Please find below some of the tutorials/tools shared on my website:
- Tutorials from my Journal Club: http://tinyurl.com/JCBioinformatics
- Linux command line exercises for NGS processing: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html
- R code for ecological data analysis: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/ecological.html
- Fancy One-liners: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html
- Scripts for Annotation: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/annotation.html
- Illumina Amplicons Analysis Workflow: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/Illumina_workflow.html
- Whole-genome Shotgun Metagenomic Sequencing Analysis: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/Metagenomics_tutorial.html
- Shell utilities for QC of FASTQ/FASTA files: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/QC.html
- Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS): http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/subsetFASTAFASTAQ.html
- Shell wrappers for EMBOSS utilities: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/emboss.html
- Metaproteomics Data Analysis: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/Metaproteomics.html
- PHYLOmap: https://bitbucket.org/umerijaz/phylomap/src
- HEATcloud: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/HEATcloud_v0.1/HEATcloud.html
- SUMMARIZEplot: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/summarize_v0.2/summarize.html
- PHYLObar: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/PHYLObar_v0.1/PHYLObar.html
- NMGS: https://github.com/microbiome/NMGS
- CONCOCT: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/CONCOCT.html
- SEQenv: https://bitbucket.org/seqenv/seqenv/src
- TAXAassign: https://github.com/umerijaz/TAXAassign
Best Wishes,
Umer
Last Edited: 06/04/2015
• 14,905 views
•
link
updated
by
Ram
•
written
by
umer.zeeshan.ijaz
•
written
by
umer.zeeshan.ijaz
2 answers
Please note that I have uploaded the following tutorial to give an introduction to Awk, BioAwk as well as how to generate statistics from metagenomics samples:
http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html
Best Wishes,
Umer
• 0 views
•
link
updated
by
Ram
•
written
by
umer.zeeshan.ijaz
•
written
by
umer.zeeshan.ijaz
Please find another tutorial on how to link metagenomic contigs using coverage and composition here: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/CONCOCT.html
Best Wishes,
Umer
• 0 views
•
link
updated
by
Ram
•
written
by
umer.zeeshan.ijaz
•
written
by
umer.zeeshan.ijaz
Log in to answer this question.
More posts like this
-
Job: Bioinformatics PDRA Opportunity in Environmental' Omics Lab (Water & Environment Research Grou…
written by umer.zeeshan.ijaz
-
Tool: R code for ecological data analysis
written by umer.zeeshan.ijaz
-
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs…
written by umer.zeeshan.ijaz
-
Tool: Shell utilities for QC of FASTQ/FASTA files (based on perl one-liners)
written by umer.zeeshan.ijaz
Interesting. May I offer a suggestion?
Turn most onliners into multiline shell scripts with documentation and store them in a GitHub repository. The concept of one-liner promises simplicity and transparency. But beyond a certain point a multiline code is a better solution.
Right now I see impressive but also scary looking long lines of code that are difficult (impossible?) to document.
They feel very black-boxy and with very little information on what is going on.
Yes, your tutorial is very informative, but Github's gist feature is made for exactly what Istvan is discussing.
Many thanks for your suggestions. Yeah, I intend to document everything in as much detail as possible, and hopefully in a few days, I'll have a much clearer explanation (I wrote all of these tutorials in a hurry). I also like the idea of putting everything on github. I'll explore that too :)