Compressing FASTA files

                                             Relative sizes of a .fasta file generated with Illumina Novaseq WGS 30x coverage.

                                               Showing the benefit of using --reference or --REFERENCE

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$ genozip --reference hs37d5.fa.gz short-reads.fa.gz

genozip short-reads.fa.gz : Done (2 minutes 50 seconds, FASTA compression ratio: 22.7 - better than .fa.gz by a factor of 5.5)
testing: genounzip short_reads.fa.gz : verified as identical to the original FASTA

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$ ls -lh short-reads.fa.*

-rw-rw-r--+ 1 3.9G May 13 04:04 short_reads.fa.genozip
-rw-rw-r--+ 1 21G May 13 02:20 short_reads.fa.gz

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Note: when a particular FASTA file is used as a reference for the first time, genozip produces a .ref.genozip file which is placed in the same directory as the FASTA. If you already have a .ref.genozip file - you can use it as an argument to

--reference instead of the FASTA. You can also generate a .ref.genozip file explicitly with (for example):

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$ genozip --make-reference hs37d5.fa.gz

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Note: genounzip needs the same reference file for decompression. It looks for it at the same location as the reference file used for genozip. Alternatively, use can use --reference to point to it directly, or set $GENOZIP_REFERENCE to point to either the file or the directory containing the file.

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Note: If you do not want genounzip to require an external reference file, you may compress with --REFERENCE instead of

--reference, which would store the relevant parts of the reference file data within the compressed file. This would obviously cause the compressed file to be larger.

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Note: using --reference is only useful for compressing FASTA files that consist of short reads. It is ignored for other types of FASTAs.

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Note: If the species has multiple versions of its reference genome FASTA, any one of them will work. For example, for human data, one option would be to use hs37d5.fa.gz.

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Note: If there is no reference genome for the target species, a reference genome of a closely related species may still work better than no reference at all. 

Note: For meta-genomic applications, it is possible to use a reference FASTA that contains sequences from multiple species, up to a total of 4 Gbp.

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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.

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

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Note: --grep, --grep-w, --regions and --regions-file require the file to be indexed during compression (only applicable when compressing FASTA files). This can be achieved by adding the --index option when compressing. However, please be aware that --index sometimes negatively impacts compression, and in particular, --reference is ignored. --index is automatically set for files which contain up to 10,000 sequences which are assembled contigs (i.e. not sequencing reads).

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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.  Their primary use is 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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Note: A reference file is also created implicitly when a FASTQ, SAM/BAM/CRAM, VCF or FASTA file, is compressed with the --reference or --REFERENCE option and with a FASTA filename as an arugment or the option.

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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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