How to do stuff
- I write these quick notes as reminders.
- Disclaimer - some could be outdated or wrong!
- I use tools on my Mac, in the terminal.
- Some tools depend on different python versions (2.x or 3.x) so it can be simpler to install them in different conda environments.
- For large analyses I connect to a server or virtual machine. These can usually use conda too.
Recently added
All
- agb - view assembly graphs with .gv extension
- artemis - view genome snps and annotations
- assembly graphs - what are they; tools to view them
- assembly workflow - bacteria
- assembly workflow - plants
- AWS - set up instance, use nextflow, docker
- bandage - gfa to png on commandline
- bash - make a basic script
- bash - repeat tasks with for-loops
- bash - structure a script with defaults, functions, getopts
- bbduk - trim adapters, filter reads
- beautiful soup - text mining
- bin directories - what are they
- blast - compare sequences to a database
- cat - concatenate reads into one file
- circlator - orient bacterial chromosomes
- conda - create environments with certain tool sets
- cores-threads-cpus-sockets - what is what
- dos2unix - fix a corrupted file
- fastERq-dump - faster version of fastq-dump
- fastp - trim adapters, filter, get stats on fastq reads
- fastq-dump - get fastq files
- fastqc - get fastq read quality info
- file formats - one line descriptions
- filtlong - filter nanopore reads
- genomescope - estimate allele proportions with a kmer profile
- git and gitHub - customise config, set up repos
- html - elements and their tags
- jellyfish - count kmers to estimate genome size
- kraken - identify a taxon
- nanofilt - filter out low quality nanopore reads
- nanostat - nanopore fastq stats
- NCBI BioProjects - how are samples and assemblies linked
- nectar cloud - how to set up a VM
- nextflow - create a workflow
- nextflow - run with a docker container
- PATH variable - what is it
- pigz - compress fastq files, uncompress fastq.gz files
- porechop - trim adapters from nanopore reads
- python - how to log to screen and logfile
- python - how to read in a file
- python - list, dictionary, format string, true/false
- python - parse genbank file with biopython
- python - read in args with parse_args()
- python - run scripts in Atom or Sublime
- python - run shell cmds with subprocess, save, pipe
- python - structure a script with main, parse_args, subprocess
- python - use init/self to define object's default values
- python - use recursion to make a Collatz sequence
- python - use recursion with global variables
- python - use regex to find text that matches patterns
- python - why can't python find the pip installed module
- read alignment vs mapping
- samtools tview - view mapped reads in the terminal
- scp - copy/move files/dirs between server/VM/local
- seqkit stats - get stats for reads or assemblies
- seqtk - get fastq stats; subsample reads
- singularity - use containers to run tools
- slurm - schedule jobs on a server
- splice junctions - what are they
- tar or untar - get files into or out of a tar file
- tool help - check if installed; get tool info
- tree - show folders and files in tree structure
- Unix - useful commands
- What not to do