usage: align [-h] [--columns N] [--max-dist N] [--min-score N]
[--print-progress] [--start-pos [1:2]:N] [--moving-average-tsv]
[--moving-average-width N] [--chart]
[--just-print-copyable-alignment]
[rc:]ACTG|path[:id] [:rc]ACTG|path[:id]
Align sequences and show them vertically interleaved
positional arguments:
[rc:]ACTG|path[:id] First input. Either a literal sequence or a path to a
fasta or fastq file. If a path, optionally include a
colon-separated id to refer to identify a specific
record in the file.
[:rc]ACTG|path[:id] Same as first input.
options:
-h, --help show this help message and exit
--columns N How many columns to wrap at. If unspecified,
autodetects.
--max-dist N How hard to try to avoid over-alignment when blocks
have been substituted out.
--min-score N Minimum score of alignment to print.
--print-progress Mark lines with how far along the genomes they
represent.
--start-pos [1:2]:N Start position, as bases into either sequence 1 or 1
--moving-average-tsv Instead of printing bases, output a tsv of how well
these genomes align.
--moving-average-width N
Standard deviation of the moving average. Ignored
unless --moving-average-tsv.
--chart visualize the alignment with some squiggles
--just-print-copyable-alignment
Ignore any other settings and just use the default
BioPython alignment pretty printing
Usage: ./siz2fastq [-z] out1.fastq[.gz] out2.fastq[.gz]
Options:
-z Compress output with gzip
Convert zstd-compressed interleaved fastq to paired (optionally gzip-compressed) fastq.
Unlike full fastq, hard wrapping is not permitted: this simply takes the first
four lines and puts them in output_1.fastq.gz, then the next four and puts
them in output_2.fastq.gz, and then keeps alternating.
Compatible with streaming. For example:
aws s3 cp s3://bucket/foo.fastq.zstd | \
siz2fastq -z >(aws s3 cp - s3://bucket/foo_1.fastq.gz) \
>(aws s3 cp - s3://bucket/foo_2.fastq.gz) \