Suggestion to improve user manual

[TrentBrick]

In the manual under the bowtie2-inspect section, you should make it clear that when indexing files bowtie creates 6 different files, for example: lambda_virus.1.bt2 lambda_virus.2.bt2 lambda_virus.3.bt2 lambda_virus.4.bt2 lambda_virus.rev.1.bt2 lambda_virus.rev.2.bt2. And that the 'base name' means to just enter in 'lambda_virus'.

I am new to bowtie and have spent an hour trying to bowtie2-inspect some existing index files I was given and kept trying to specify one and only one of the index files rather than their 'base'.

I have now seen that in the bowtie-build section you state that 6 index files are generated but maybe even pointing readers of the bowtie-inspect section to this would help? This was the only section of the guide that I skipped ahead of and it clearly left me very lost as a result.

This is just a suggestion, sorry if this should not be in the issues section of the github repo. And thanks for creating bowtie2.