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software:topical:lifescience [2018/09/25 14:19]
meesters [NGS Preprocessing Software]
software:topical:lifescience [2020/02/11 19:13] (current)
meesters [Various -- Software Collections]
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 **Contributing** **Contributing**
  
-Yes, please! Please get in touch with us, if you want to benchmark or contribute wrapper scripts. We created some [[https://​gitlab.rlp.net/​hpc-jgu-lifescience|repositories]] and would be delighted to add your name to the contributors. Also, contributions to this wiki (reports, suggestions,​ error notes) are welcome!+Yes, please! Please get in touch with us, if you want to benchmark or contribute wrapper scripts. We created some [[https://​gitlab.rlp.net/​hpc-jgu-lifescience|repositories]] and would be delighted to you to the list of contributors. Also, contributions to this wiki (reports, suggestions,​ error notes) are welcome!
 </​WRAP>​ </​WRAP>​
-===== NGS & Co. ===== 
  
-==== Divide & Conquer ​====+===== Installed Life Science Software =====
  
-  * [[software:​topical:​lifescience:​splitting|Splitting FASTQ files]]+Life science software is installed on Mogon I and II in the ''​bio'' ​[[:software|module category]]((This is true with a few exceptions, e.g. AutoDock.)). ​
  
-==== NGS Preprocessing Software ====+To list the available tools, you can type:
  
-  * [[software:​topical:​lifescience:​trimmomatic|Quality Check (Adapter- ​& Quality ​Trimming) with Trimmomatic]] +<code bash> 
-  * [[software:​topical:​lifescience:​flexbar|flexbar]]+module av bio/ |& cut -f2 -d '/'​ | uniq 
 +</​code>​ 
 + 
 +A subsequent  
 +<code bash> 
 +module av|& grep <tool of interest>​ 
 +</​code>​ 
 +, where ''​tool of interest''​ is copy-pasted from the output above, will show the respective versions for that software. 
 + 
 +You can ask for updates on a particular software or to install previously not supported software [[https://​hpc.uni-mainz.de/​high-performance-computing/​service-angebot/​softwareinstallation/​|via our webpage]]. 
 + 
 +<WRAP center round info 90%> 
 +If an installed tool is not listed on this page, respectively its underlying links, you may contribute this (its a wiki!) or ask for further documentation. 
 +</​WRAP>​ 
 + 
 +===== R and Bioconductor ===== 
 + 
 +The information on R and Bioconductor merits a [[software:​topical:​lifescience:​R_Bioconductor|separate page]]. 
 + 
 +===== NGS Co. ===== 
 + 
 + 
 +==== NGS Preprocessing Software and other Quality ​Checks ==== 
 + 
 +  * [[software:​topical:​lifescience:​QA|Quality Assessment Tools]] 
 +  * [[software:​topical:​lifescience:​QC|Quality Check (Adapter- & Quality Trimming)]]
  
 ==== Mapping Tools ==== ==== Mapping Tools ====
  
-  * [[software:​topical:​lifescience:​ngs_read_mapping_tools|NGS Read-Mapping Tools: BWA, Bowtie and STAR]]+  * [[software:​topical:​lifescience:​ngs_read_mapping_tools|NGS Read-Mapping Tools]]
  
-==== Annotation ​Tools ====+==== Variant Calling ​Tools ====
  
-  * [[software:​topical:​lifescience:​blast|BLAST]] +  * [[software:​topical:​lifescience:​variant_calling_tools|Variant Calling Tools]] 
-  * [[software:​topical:​lifescience:​blast|Diamond]]+==== Intermediate Processing ====
  
-==== Various -- Software Collections ====+  * [[software:​topical:​lifescience:​sdi|Sorting,​ Deduplication and Indexing of BAM files]]
  
-  ​[[software:​topical:​lifescience:​seqan|SeqAn]] ​-- efficient applications of different areas * +==== *-Seq Analysis ====
-  * [[software:​topical:​lifescience:​bbmap|BBMap]] -- short read aligner + other tools *+
  
-===== Genome Assembly ​=====+  * [[software:​topical:​lifescience:​transcript_abundance_tools|Assessing Transcript Abundance]] 
 + 
 +==== Annotation Tools / Local Search Tools ==== 
 + 
 +  * [[software:​topical:​lifescience:​local_search_tools|Local Search Tools (BLAST & Co.)]] 
 + 
 + 
 +==== Various -- Software Collections ==== 
 + 
 +  * [[software:​topical:​lifescience:​seqan|SeqAn]] -- efficient applications of different areas  
 +  * [[software:​topical:​lifescience:​bbmap|BBMap]] -- short read aligner + other tools  
 +  * [[software:​topical:​lifescience:​sra|SRA toolkit]] -- the NCBI SRA toolkit on mogon
  
-  * [[software:​topical:​lifescience:​trinity|Trinity]] * 
  
 ===== Evolutionary & Phylogenetics Software Tools ===== ===== Evolutionary & Phylogenetics Software Tools =====
  
 +  * [[software:​topical:​lifescience:​genome_assembly|Genome Assembly Tools]]
 +  * [[software:​topical:​lifescience:​phylogenic_reconstruction|Phylogenetic Reconstruction]]
 +  * [[software:​topical:​lifescience:​multiple_sequence_alignment|Multiple Sequence Alignment]]
 +  * [[software:​topical:​lifescience:​population_genetics|General Population Genetics]]
  
-  * [[software:​topical:​lifescience:​ipyrad|IPyrad]] 
  
 ===== Molecular Docking Tools ===== ===== Molecular Docking Tools =====
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   * [[software:​topical:​physics:​vmd_namd|Using VMD and NAMD on Mogon]]   * [[software:​topical:​physics:​vmd_namd|Using VMD and NAMD on Mogon]]
  
 +===== Single Particle Processing / Analysis =====
 +
 +  * [[software:​topical:​lifescience:​cistem|Using cisTEM]]
 +  * [[software:​topical:​lifescience:​relion|Using RELION]]
 +
 +===== Development =====
 +
 +  * [[software:​topical:​lifescience:​seqan3|The SeqAn C++ library for sequence analysis]]
  
 ===== What Else? ===== ===== What Else? =====
  
-This wiki does not cover your topic / favourite ​software? Please let us know.+This wiki does not cover your topic / favorite ​software? Please let us know.
  
   - We can install [[https://​hpc.uni-mainz.de/​high-performance-computing/​service-angebot/​softwareinstallation/​|your software]], which frequently is better than to install software yourself((With the exception of abandonware,​ crappy software, scripts which can be installed with ''​pip'',​ ''​cran'',​ etc..)), because:   - We can install [[https://​hpc.uni-mainz.de/​high-performance-computing/​service-angebot/​softwareinstallation/​|your software]], which frequently is better than to install software yourself((With the exception of abandonware,​ crappy software, scripts which can be installed with ''​pip'',​ ''​cran'',​ etc..)), because:
     * we install software in an optimized fashion     * we install software in an optimized fashion
     * if installed as a module, we made the commitment to support the software, if there are issues with the module, the batch system or I/O((but, of course, not with respect to bugs within the software))     * if installed as a module, we made the commitment to support the software, if there are issues with the module, the batch system or I/O((but, of course, not with respect to bugs within the software))
-  - Writing wrapper scripts for otherwise non-performant applications can be cumbersome. We still encourage to approach us and ask us, before being stuck in a project.+  - Writing wrapper scripts for otherwise non-performant applications can take time. We still encourage to approach us and ask us, before being stuck in a project.
  
-Any contribution (a script, an idea, a reported issue, documentation,​ test data, own benchmark, etc.) is welcome! Particularly links labeled with "​*"​ require attention((Missing links wait to be filled with content - a re-structuring might also occur.)).+<WRAP center round info 90%> 
 +Any contribution (a script, an idea, a reported issue, feature request, documentation,​ test data, own benchmark, etc.) is welcome! Particularly, section ​links labeled with "​*"​ require attention((Missing links wait to be filled with content - a re-structuring might also occur.)). 
 + 
 +  * [[https://​mogonwiki.zdv.uni-mainz.de/​dokuwiki/​training_and_outreach:​faq#​may_i_contribute_to_this_wiki|Here is info on how to contribute to documentation]]. 
 +  * If you have written a piece of software (e.g. a script for a particular workflow) you would like to share, please [[hpc@uni-mainz.de|do not hesitate to approach us]]. 
 +</​WRAP>​ 
 + 
 +<WRAP center round info 90%> 
 +**Tired of //​[[https://​en.wikipedia.org/​wiki/​Software_as_a_service|Software as a Service]]//?​** 
 + 
 +  * You have the option to collaborate on specific setups or if a specific tool needs to be written. 
 +  * Any feedback will help. 
 +</​WRAP>​
            
software/topical/lifescience.1537877974.txt.gz · Last modified: 2018/09/25 14:19 by meesters