UCSF Francis Lab

Pseudo Pipeline and Topic Notes

• AWS
• C4

• ---

• AlphaFold
• EV
• Demultiplex
• Preprocessing
• DNASeq
• RNASeq
• RNAStrandedness
• miRNA
• APOBEC
• Aligners
  • Bowtie2
  • Bowtie
  • BWA
  • STAR
  • Blat
  • Blast
  • Diamond
  • Kraken
  • Kallisto
  • Salmon
• VCF
• K-mer Analysis
  • iMOKA
  • GECKO
  • HAWK
  • MetaGO
• Repeat / Transposable Elements
  • MELT
  • REdiscoverTE
  • TEfinder
  • xTea
  • GeneTEFlow
  • SQuIRE
  • RepEnrich2
  • TEtools
  • McClintock
  • TEtranscripts
  • TEProF2
• Computing Resources, Cloud Services and Data
  • General Cloud
  • C4
  • TIPCC
  • AWS
  • eRA Commons
  • UK BioBank RAP
  • SGDP
  • CGC
  • St Jude
  • LatchBio
  • Use Galaxy
  • TCGA
  • TARGET
  • GTEx
  • dbGaP
  • Seven Bridges
  • 1000 Genomes
• Assemblers
• Box
• Catchitt
• Chimera
• CIRCexplorer2
• Dark
• DiscordRetro
• ERVCaller
• Features
• GWAS
• GuideSeq
• HLA
• Illumina
• Imputation
• Manta_Strelka
• Masking
• References
• SNP2HLA
• Taxonomy
• TelSeq
• hervQuant
• Sleuth
• DESeq
• Long Read / ONT
• Phage Display
• TensorFlow
• KMC
• UMI
• Cutadapt
• Notebooks
  • Jupyter
  • Rmarkdown
• Tools
  • Singularity
  • Docker

General

• UCSF Github Repos
• UNR Github Repos
• Cal Github Repos
• Jake's Github Repos

Helpful links

• C4 - Research Computing at Scale
• TIPCC - a High-Performance Compute Environment at UCSF
• Wynton HPC
• AWS Cloud Credits for Research
• Github Pages