Bioinformatics tips tricks workflows
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This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts).
A list of tutorials, workflows, and recipes
- Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly
- A Perl script to convert fastq to fasta file format
- Mapping Pair-end reads with Stampy
- Create slices from a collection of BAM files
- Setting up and using a virtual environment for Python3
- ssh without password
- Create a shortcut for the ssh log-in command
- Installing R packages locally
- Command-line tricks for manipulating fastq files
- Assemble mitochondrial genomes from whole-genome short-read data
- 1000 Bulls mapping pipeline at ABGC
- Animal Breeding and Genomics Sequence Archives (ABGSA)
- Pig mapping pipeline at ABGC
- Extract a set of pig SNPs not called in a control sample (soybean)
- Calculate nucleotide diversity (theta) corrected for sequencing depth
- RNA-seq analysis with Tophat
- Variant annotation tutorial
- Issues with ASReml
- Checkpointing
- Assembly and Annotation guidelines (denovo)
- DE expression analysis with tophat2 / cuffdiff
- JBrowse
- Running Snakemake pipelines
- Mapping and variant calling pipeline
- Population structural variant calling pipeline
- Population mapping pipeline
- Nanopore assembly and variant calling pipeline
- Population variant calling pipeline