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10.0 years ago
umer.zeeshan.ijaz
★
1.8k
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
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 :)