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Page 23 of 43

Not secure

Change call to samtools.

Not secure

Added `--tempdir` argument to `run-bowtie2.py`.

Not secure

Added `make-consensus.py` script and tests (for a new `dark/bowtie2.py`
file). Upgraded `run-bowtie2.py`.

Not secure

Added `--picard` to `run-bowtie2.py` command to allow removal of duplicates
found by Picard.

Not secure

Added `run-bowtie2.py` command.

Not secure

Make `compare-sequences.py` fall back to use `stretcher` if the call to
`needle` fails because the sequences are too long.

Has known vulnerabilities

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