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software:topical:lifescience [2019/04/12 08:15]
meesters [What Else?]
software:topical:lifescience [2020/02/11 19:13] (current)
meesters [Various -- Software Collections]
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 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]]. 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. =====
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   * [[software:​topical:​lifescience:​ngs_read_mapping_tools|NGS Read-Mapping Tools]]   * [[software:​topical:​lifescience:​ngs_read_mapping_tools|NGS Read-Mapping Tools]]
  
 +==== Variant Calling Tools ====
 +
 +  * [[software:​topical:​lifescience:​variant_calling_tools|Variant Calling Tools]]
 ==== Intermediate Processing ==== ==== Intermediate Processing ====
  
   * [[software:​topical:​lifescience:​sdi|Sorting,​ Deduplication and Indexing of BAM files]]   * [[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 ==== ==== Annotation Tools / Local Search Tools ====
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 ==== Various -- Software Collections ==== ==== Various -- Software Collections ====
  
-  * [[software:​topical:​lifescience:​seqan|SeqAn]] -- efficient applications of different areas * +  * [[software:​topical:​lifescience:​seqan|SeqAn]] -- efficient applications of different areas  
-  * [[software:​topical:​lifescience:​bbmap|BBMap]] -- short read aligner + other tools *+  * [[software:​topical:​lifescience:​bbmap|BBMap]] -- short read aligner + other tools  
 +  ​[[software:​topical:​lifescience:​sra|SRA toolkit]] -- the NCBI SRA toolkit on mogon
  
-===== Genome Assembly ===== 
- 
-  * [[software:​topical:​lifescience:​genome_assembly|Genome Assembly Tools]] 
  
 ===== 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? =====
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   * [[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]].   * [[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]].   * 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>​ </​WRAP>​
            
software/topical/lifescience.1555049738.txt.gz · Last modified: 2019/04/12 08:15 by meesters