Compressing
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$ genozip chm13.draft_v1.1.fasta.gz
genozip chm13.draft_v1.1.fasta.gz : Done (15 seconds, FASTA compression ratio: 4.8 - better than .fasta.gz by a factor of 1.4)
testing: genounzip chm13.draft_v1.1.fasta.genozip : verified as identical to the original FASTA
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$ ls -lh chm13.draft_v1.1.*
-rw-rw-r--+ 1 divon divon 617M Aug 5 00:05 chm13.draft_v1.1.fasta.genozip
-rw-rw-r--+ 1 divon divon 852M May 8 2021 chm13.draft_v1.1.fasta.gz
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Uncompressing
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$ genounzip chm13.draft_v1.1.fasta.genozip
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Viewing and analyzing
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$ genocat chm13.draft_v1.1.fasta.genozip
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genocat options:
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--sequential : each sequence is output in single line - newlines are removed.
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--header-only: shows only the description lines (no sequences).
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--no-header: shows only the sequences, omitting the description lines.
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--header-one: shows the description lines truncated at the first space or tab character.
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--grep string: shows only the sequences in which string is contained in the header.
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--grep-w string: same as --grep, but string must match a whole word.
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--regions sequence-name[,sequence-name2...] shows only the sequences requested. sequence-name is the prefix of the description line up to the first space, tab or newline.
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--regions-file filename same as --regions, but list of sequence names is taken from a file.
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--head[=lines] show line lines from the top of the file. This is similar to piping genocat | head but faster.
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--tail[=lines] similar to --head but shows lines from the end of file.
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--lines [first]-[last] or [first] shows a range of lines.
--phylip view the data in PHYLIP format, see: Converting MultiFASTA to PHYLIP and back.
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--taxid filter sequences by species using kraken2 data, See Filtering with Kraken.
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--downsample rate[,shard] technically works on FASTA files, but usually not very useful. See Downsampling.
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Generating a Genozip reference file from a FASTA file
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A FASTA file may be used to generate a Genozip reference file, using the --make-reference option:
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$ genozip --make-reference chm13.draft_v1.1.fasta.gz
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Reference files are a file format used in Genozip internally, and cannot be uncompressed. They are also created implicitly when files, such as FASTQ, BAM or VCF, are compressed with the --reference or --REFERENCE options.
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The main role of reference files is to be used for compressing other files, using the --reference or --REFERENCE options, which usually results in significantly improved compression.
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However, In addition to their primary use, reference files are also useful for analyzing the underlying FASTA: they can be used to easy view sub-sequences of contigs in certain regions (forward or reverse complemented) using --regions and --regions-file, for finding IUPAC non-ACGTN pseudo-bases in the file with --show-ref-iupacs, and seeing properties of the contigs with --show-ref-contigs. See more here: Reference file options.
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For a full list of options, see the genozip command line reference
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Questions? support@genozip.com
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