Reference

Output modes¶

Strobealign has three output modes that differ in speed and how much information about each read is available:

• Extension alignment mode is the default. The program outputs aligned reads in SAM format.

• Mapping-only mode is enabled with -x. It is faster because no base-level alignments are computed. Output format is PAF.

• Abundance estimation mode is enabled with --aemb. No read-level information is output, only a table with per-contig abundances.

Command-line options¶

Please run strobealign --help to see the most up-to-date list of command-line options. Some important ones are:

• -r: Mean read length. If given, this overrides the read length estimated from the input file(s). This is usually only required in combination with --create-index, see index files.

• -t N, --threads=N: Use N threads (both for mapping and indexing).

• --eqx: Emit = and X CIGAR operations instead of M.

• -x: Only map reads, do not do no base-level alignment. This switches the output format from SAM to PAF.

• --aemb: Output estimated abundance value of each contig, see section above.

• --rg-id=ID: Add RG tag to each SAM record.

• --rg=TAG:VALUE: Add read group metadata to the SAM header. This can be specified multiple times. Example: --rg-id=1 --rg=SM:mysamle --rg=LB:mylibrary.

• -N INT: Output up to INT secondary alignments. By default, no secondary alignments are output.

• -U: Suppress output of unmapped single-end reads and pairs in which both reads are unmapped.

• --use-index: Use a pre-generated index instead of generating a new one.

• --create-index, -i: Generate a strobemer index file (.sti) and write it to disk next to the input reference FASTA. Do not map reads. If read files are provided, they are used to estimate read length. See index files.