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software:topical:lifescience [2018/08/24 12:27]
meesters [NGS Preprocessing Software]
software:topical:lifescience [2020/02/11 19:13] (current)
meesters [Various -- Software Collections]
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   * Benchmarks displayed on these pages are only benchmarks with respect to speed. The values are valid only for the given parameters and may greatly vary for deviating parameters or input. (You may indicate deviating experiences to us.)   * Benchmarks displayed on these pages are only benchmarks with respect to speed. The values are valid only for the given parameters and may greatly vary for deviating parameters or input. (You may indicate deviating experiences to us.)
   * We strive to improve the beauty and information content of this page. However, the conducted science is up to you as a user - whether or not a particular program invocation (the arguments supplied) actually make sense for your scientific question is up to you to decide.   * We strive to improve the beauty and information content of this page. However, the conducted science is up to you as a user - whether or not a particular program invocation (the arguments supplied) actually make sense for your scientific question is up to you to decide.
 +
 +**News**
 +
 +News on software in bioinformatics and related stuff is distributed via a [[https://​lists.uni-mainz.de/​sympa/​review/​bioinf-news|mailing list]] (low traffic). You can subscribe, too. You may also distribute and share information using this list. 
  
 **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>​
 +
 +===== Installed Life Science Software =====
 +
 +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.)). ​
 +
 +To list the available tools, you can type:
 +
 +<code bash>
 +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 & Co. =====
  
-==== NGS Preprocessing Software ==== 
  
-  ​* [[software:​topical:​lifescience:​trimmomatic|Trimmomatic]] +==== NGS Preprocessing Software and other Quality Checks ==== 
-  * [[software:​topical:​lifescience:​ncap|NCAP]]+ 
 +  ​* [[software:​topical:​lifescience:​QA|Quality Assessment Tools]] 
 +  * [[software:​topical:​lifescience:​QC|Quality Check (Adapter- & Quality Trimming)]]
  
 ==== Mapping Tools ==== ==== Mapping Tools ====
  
-  * [[software:​topical:​lifescience:​bwa|BWA]] +  * [[software:​topical:​lifescience:​ngs_read_mapping_tools|NGS Read-Mapping Tools]]
-  * [[software:​topical:​lifescience:​bowtie|Bowtie (1/2)]] +
-  * [[software:​topical:​lifescience:​star|STAR]]+
  
-==== 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 ====
  
-===== Phylogenetics Tools =====+  * [[software:​topical:​lifescience:​sdi|Sorting,​ Deduplication and Indexing of BAM files]]
  
 +==== *-Seq Analysis ====
 +
 +  * [[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
 +
 +
 +===== 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]]
  
  
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 ===== Molecular Dynamics Simulations ===== ===== Molecular Dynamics Simulations =====
  
-Molecular Dynamics (MD) simulations are not confined to condensed matter physics, but of interest in the life sciences as well. They are, however, thematically attributed to physics. This page, therefore, merely indicates ​some links:+Molecular Dynamics (MD) simulations are not confined to condensed matter physics, but of interest in the life sciences as well. They are, however, thematically attributed to physics. This page, therefore, merely indicates ​a link:
  
   * [[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, 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 commitment ​-- or put negatively: it is not possible ​to support software ​someone has installed somehowdue to the ever annoying lack of crystal balls. +    * 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, reported issue) is welcome!+<WRAP center round info 90%> 
 +Any contribution (a script, an idea, 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.1535106465.txt.gz · Last modified: 2018/08/24 12:27 by meesters