Genome indexing

Question

[Roy.anupama11]

What are the different tools we can use for genome indexing?

Thanks

[Marco Pannone]

Very vague question, it depends on what you are going to do afterward.

Supposing you have a genome in .fasta format and you are going to align some sequencing data, you need to index it with the specific tool you are using for alignment.

Examples: Bowtie2; HISAT2.

[Roy.anupama11]

Actually I came across Picard (https://github.com/broadinstitute/picard) and BWA. I wanted to re-confirm. Since I never used both. I have used HISAT2. Instead of BWA, can I use HISAT2?

[Marco Pannone]

What type of data do you have? RNA-seq?