map command

Maps unpaired reads to a reference genome. The reference genome is stored as a UFI file created by the make_ufi command. The original FASTA file for the reference is not needed.

Reads must be in FASTQ format or gzip-compressed FASTQ format. It is generally faster to use uncompressed reads because decompression is typically more expensive than the additional file i/o time required to read the larger uncompressed file.

Options
The FASTQ filename is specified following -map. Use "-" (minus sign) to get input from a pipe. If the reads are gzip-compressed, the filename must end in .gz. Piped input must be decompressed (you can always add gunzip to the pipe if needed).

The reference genome index filename is given by the -ufi option.

A filename for SAM format output is specified by -samout. Use /dev/stdout or "-" (minus sign) if you want to pipe output to another program.

The -threads option specifies the number of processor threads to use for mapping. Default is the number of CPU cores or 10, whichever is smaller.

The -veryfast option specifies a variant mapping algorithm which is ~3x faster but somewhat less accurate. To get the full speed improvement, the index should also be built with the -veryfast option, though UFI indexes are compatible with map regardless of whether -veryfast is used for mapping or for indexing.

Pipes
To get input from a pipe, use /dev/stdin as the filename.

To send output to a pipe, use "-" (minus sign) as the filename. Using /dev/stdout will not work because urmap attempts to create the file.

Example

urmap -map reads.fastq -ufi hg38.ufi -samout reads.sam