Alignment with Giraffe (index)

We have several wiki pages on Giraffe.

• Mapping short reads with Giraffe
• Mapping long reads with Giraffe
• Giraffe best practices: General reference for how to use Giraffe.
• Giraffe troubleshooting: how to read Giraffe's --show-work debug logs.
• Long‐read RNA‐seq with pre‐existing pangenome: Tutorial including the use of Giraffe to align long RNA-seq reads.
• Graph & annotations for two E. coli strains: Tutorial including the use of Giraffe to align an assembly onto a pre-existing graph