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Top/start page for documentation of:

1. Data files naming rules (draft)

   • file & sample naming

2. hardware

   • servers, workstations, etc.

3. software

   • bioinformatics software
     • General
       • varia
     • NGS software
       • NGS general utils
         • ngs_utils_all
       • NGS mapping
         • DNA
         • RNA
         • Methylation
       • Mutations
         • SNP etc
         • annotation
         • structural variation
         • CNV software (genotyping & NGS)
         • virus detection
       • RNA-seq quantification
         • RSEM
         • DESeq2
       • kinship tools
         • akt from Illumina
     • statistical
       • R_packages
     • other
       • pedigree draw
     • arrays
       • illumina soft
   • old software
     • synthesis

4. data

   • formats
     • fastq
   • locations
   • metadata/descriptions

5. users

   • empty

6. tips for data processing FAQ

   • merging fastq
   • rsync data using ssh

7. software 2

   • operating systems
     • Linux / Unix
       • real hardware
         • Debian empty
         • Manjaro empty
         • Synology DSM empty
       • virtual machines
         • Mx Linux empty
         • Manjaro empty
         • FreeNAS empty
       • varia ( rescue, security checks, containers, clusters, 2 watch & consider, etc.)
         • Gparted (rescue/partition resize) https://gparted.org/livecd.php
         • Kali (security testing)
         • Alpine (containers minimal distro)
         • Clear Linux from Intel (speed, clusters, containers)
         • Raspbian (RaspberryPi Debian based) for thin clients
     • Windows
       • on equipment machines
       • workstations
       • varia
         • ReactOS (NT clone) empty
         • Wine (Windows emulator on Linux) empty
   • virtual machines / containers
     • Virtual Box
     • Singularity
     • FreeNAS test empty
   • clustering, pipelines
     • slurm
     • NextFlow
     • snakemake empty
     • monitoring empty
   • databases
     • SQL
       • postgresql
       • mariadb empty
       • mysql
       • sqlite
       • DB access soft empty
     • noSQL
       • MongoDb empty
       • neo4j empty
     • varia empty
   • big packages
     • galaxy (bioinfo) empty
     • GitLab empty
     • Taiga (collab, on hold) empty
     • openERP (legacy) empty
   • network/computer connection software
     • VPN etc.
     • file transfer & sharing
     • security empty
   • software development
     • compilers
     • interpreters empty
     • editors empty
     • static analysis empty
     • debugging empty
     • source control empty
     • varia empty