combine

Combine individual indices from the same sample (e.g., multiple sequencing rounds) or various samples into a single index

usage: malva combine [-h] [--index-in INDEX_IN] [--merge-chunks] [--merge-projects] [--uuid UUID] [--threads THREADS]

Named Arguments

--index-in

Valid directory where the malva indices are located as subdirectories.

The new combined index (and metadata) will be stored at this folder.

--merge-chunks

When the chunk size is less than the number of total reads, there will be

several separate chunks in the index file. When this option is provided, the different chunks are merged into a single one, which will reduce index size and improve query speed. This adds a bit of time to the overall processing.

Default: False

--merge-projects

Merge data from different projects, preserving project identities

Default: False

--uuid

When merging projects, this is a file with one UUID per line (in order, will assign the integer project ID)

--threads

Number of threads used for parallel processing

Default: 1