Silva reference files

If you use the SILVA reference files you should be aware of their dual-use license that covers Release 132 and earlier.

Release 138.2

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. In our published opinion, this is the best reference alignment out there - far superior to the greengenes or RDP alignments. It’s unclear why this version of the release is smaller than previous releases. We have prepared a README document where you can read about the process that we used to generate these references. This is also the first SILVA release that is available under the CC-BY license opening the data up to commercial use

  • Full-length sequences and taxonomy references (145520 bacteria, 3744 archaea, and 15032 eukarya sequences). This reference could be customized for alignments, but could also be used for classification. The uncompressed version is ~7.7 GB and the compressed version is 270 MB.
  • recreated seed database (6727 bacteria, 133 archaea, and 1847 eukarya sequences). The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database that have a 100% quality score to the SEED alignment (field ‘align_ident_slv’ in the arb database) and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing a composite dataset for bacterial, archaeal, and eukaryotic sequences. The uncompressed version is 416 MB and the compressed version is 15 MB.
  • Silva-based alignment of template file for chimera.slayer (5,181 sequences)

Release 138.1

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. In our published opinion, this is the best reference alignment out there - far superior to the greengenes or RDP alignments. It’s unclear why this version of the release is smaller than previous releases. We have noticed some weird results using this version of the SEED alignment relative to previous versions of the alignment. This is most likely because it is smaller than previous versions. The Schloss group is sticking with the v132 version of the SEED database for alignments. We have prepared a README document where you can read about the process that we used to generate these references. This is also the first SILVA release that is available under the CC-BY license opening the data up to commercial use

  • Full-length sequences and taxonomy references (128884 bacteria, 2846 archaea, and 14871 eukarya sequences). This reference could be customized for alignments, but could also be used for classification. The uncompressed version is ~6.8 GB and the compressed version is 241 MB.
  • recreated seed database (5736 bacteria, 81 archaea, and 1824 eukarya sequences). The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database that have a 100% quality score to the SEED alignment (field ‘align_ident_slv’ in the arb database) and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing a composite dataset for bacterial, archaeal, and eukaryotic sequences. The uncompressed version is 365 MB and the compressed version is 13 MB.
  • Silva-based alignment of template file for chimera.slayer (5,181 sequences)

Release 138

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. In our published opinion, this is the best reference alignment out there - far superior to the greengenes or RDP alignments. It’s unclear why this version of the release is smaller than previous releases. We have noticed some weird results using this version of the SEED alignment relative to previous versions of the alignment. This is most likely because it is smaller than previous versions. The Schloss group is sticking with the v132 version of the SEED database for alignments. We have prepared a README document where you can read about the process that we used to generate these references. This is also the first SILVA release that is available under the CC-BY license opening the data up to commercial use

  • Full-length sequences and taxonomy references (129063 bacteria, 2846 archaea, and 14887 eukarya sequences). This reference could be customized for alignments, but could also be used for classification. The uncompressed version is ~6.9 GB and the compressed version is 241 MB.
  • recreated seed database (5741 bacteria, 81 archaea, and 1834 eukarya sequences). The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database that have a 100% quality score to the SEED alignment (field ‘align_ident_slv’ in the arb database) and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing a composite dataset for bacterial, archaeal, and eukaryotic sequences. The uncompressed version is 366 MB and the compressed version is 13 MB.
  • Silva-based alignment of template file for chimera.slayer (5,181 sequences)

Release 132

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. In our published opinion, this is the best reference alignment out there - far superior to the greengenes alignment. In a shift from our previous version of the SILVA references, we are providing the SEED database, the full-length sequences available from the NR SILVA database, and a SILVA aligned version of the gold database that is used for reference-based chimera detection. We have prepared a README document where you can read about the process that we used to generate these references.

  • Full-length sequences and taxonomy references (188247 bacteria, 4626 archaea, and 20246 eukarya sequences). This reference could be customized for alignments, but could also be used for classification. The uncompressed version is ~9.9 GB and the compressed version is 348 MB.
  • recreated seed database (8517 bacteria, 147 archaea, and 2516 eukarya sequences). The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database (v123) that have a 100% quality score to the SEED alignment (field ‘align_ident_slv’ in the arb database) and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing a composite dataset for bacterial, archaeal, and eukaryotic sequences. The uncompressed version is 534 MB and the compressed version is 19 MB.
  • Silva-based alignment of template file for chimera.slayer (5,181 sequences)

Release 128

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. In our published opinion, this is the best reference alignment out there - far superior to the greengenes alignment. In a shift from our previous version of the SILVA references, we are providing the SEED database, the full-length sequences available from the NR SILVA database, and a SILVA aligned version of the gold database that is used for reference-based chimera detection. We have prepared a README document where you can read about the process that we used to generate these references.

  • Full length sequences and taxonomy references (168111 bacteria, 4337 archaea, and 18213 eukarya sequences). This reference could be customized for alignments, but could also be used for classification. The uncompressed version is ~8.9 GB and the compressed version is 311 MB.
  • recreated seed database (8512 bacteria, 147 archaea, and 2554 eukarya sequences). The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database (v123) that have a 100% quality score to the SEED alignment (field ‘align_ident_slv’ in the arb database) and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing a composite dataset for bacterial, archaeal, and eukaryotic sequences. The uncompressed version is 536 MB and the compressed version is 19 MB.
  • Silva-based alignment of template file for chimera.slayer (5,181 sequences)

Release 123

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. In our published opinion, this is the best reference alignment out there - far superior to the greengenes alignment. In a shift from our previous version of the SILVA references, we are now providing the SEED database, the full-length sequences available from the NR SILVA database, and a SILVA aligned version of the gold database that is used for reference-based chimera detection. We have prepared a README document where you can read about the process that we used to generate these references.

  • Full length sequences and taxonomy references (152308 bacteria, 3901 archaea, and 16209 eukarya sequences). This reference could be customized for alignments, but could also be used for classification. The uncompressed version is ~7.2 GB and the compressed version is 249 MB.
  • recreated seed database (12083 bacteria, 294 archaea, and 2537 eukarya sequences). The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database (v123) that have a 100% quality score to the SEED alignment (field ‘align_ident_slv’ in the arb database) and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing a composite dataset for bacterial, archaeal, and eukaryotic sequences. The uncompressed version is ~700 MB and the compressed version is 25 MB.
  • Silva-based alignment of template file for chimera.slayer (5,181 sequences)

Release 119

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. In our published opinion, this is the best reference alignment out there - far superior to the greengenes alignment. In a shift from our previous version of the SILVA references, we are now providing the SEED database, the full-length sequences available from the NR SILVA database, and a SILVA aligned version of the gold database that is used for reference-based chimera detection. We have prepared a README document where you can read about the process that we used to generate these references.

  • Full length sequences and taxonomy references (137879 bacteria, 3155 archaea, and 12273 eukarya sequences). This reference could be customized for alignments, but could also be used for classification. The uncompressed version is ~7.2 GB and the compressed version is 249 MB.
  • Recreated SEED database (12244 bacteria, 207 archaea, and 2558 eukarya sequences). The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database (v119) that have a 100% quality score to the SEED alignment (field ‘align_ident_slv’ in the arb database) and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing a composite dataset for bacterial, archaeal, and eukaryotic sequences. The uncompressed version is ~700 MB and the compressed version is 25 MB.
  • Silva-based alignment of template file for chimera.slayer (5,181 sequences)

Release 102

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don’t know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database (v102) that have a 100% quality score to the SEED alignment and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing separate datasets for bacterial, archaeal, and eukaryotic sequences. Within each reference set are the aligned sequence file (e.g. silva.bacteria.fasta), an unaligned sequence file (e.g. nogap.bacteria.fasta), and taxonomy outlines (e.g. silva.bacteria.silva.tax):