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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

$ 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


$ genounzip chm13.draft_v1.1.fasta.genozip

Viewing and analyzing

$ genocat chm13.draft_v1.1.fasta.genozip

genocat options:

--sequential : each sequence is output in single line - newlines are removed.

--header-only: shows only the description lines (no sequences).

--no-header: shows only the sequences, omitting the description lines.

--header-one: shows the description lines truncated at the first space or tab character.

--grep string: shows only the sequences in which string is contained in the header.

--grep-w string: same as --grep, but string must match a whole word.

--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.

--regions-file filename same as --regions, but list of sequence names is taken from a file.

--head[=lines] show line lines from the top of the file. This is similar to piping genocat | head but faster.

--tail[=lines] similar to --head but shows lines from the end of file.

--lines [first]-[last] or [first] shows a range of lines.


--phylip view the data in PHYLIP format, see:  Converting MultiFASTA to PHYLIP and back.

--taxid filter sequences by species using kraken2 data, See Filtering with Kraken.

--downsample rate[,shard] technically works on FASTA files, but usually not very useful. See Downsampling.

Multiseq FASTA files​

We define a Multiseq file as a Multi-FASTA in which we expect the sequences to be quite similar to each other. For example, a file consisting of many samples of the same virus species. 

Genozip offers some additional functionality for Multiseq FASTAs:

1. Compressing: use the --multiseq option to inform Genozip that this is a Multiseq FASTA. Genozip uses this information to improve the compression.

2. Converting to PHYLIP format: See Converting MultiFASTA to PHYLIP and back.

Reference files

A FASTA file may be compressed as a Genozip reference file, using the --make-reference option:

genozip --make-reference chm13.draft_v1.1.fasta.gz

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.

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.

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.

For a full list of options, see the genozip command line reference


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