Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly

Sign up
Appearance settings

Pre‐built Database Indexes

Hannes Hauswedell edited this page Jul 21, 2024 · 2 revisions

This page contains links to databases that are pre-formatted for use with Lambda (so that you don't have to index them yourself). If you have created indexes yourself and would like to share them, you can send us a link.

lambda3 branch

  • Unpacking the file after download is not required; you can use it as-is. However, unzipped files may load slightly faster during search (this depends on disk vs CPU speed).
  • Taxonomy information is included in some indexes, see Taxonomic Workflows for more information.
  • Memory usage during search is usually Unpacked Size + size-of-query-file ± 10%. The memory usage during the creation of the indexes was higher, around 10x input size.

Protein databases

Database Log Date Tax Download Size
⇩ Uniref90 📄 Log 20230713 145GB
⇩ Uniref50 📄 Log 20230713 44GB
⇩ Uniprot Sprot 📄 Log 20230713 0.4GB

Databases used in the paper

Database Date Tax Download Size Domain
⇩ Uniref50 20220525 38GB Protein
⇩ Human microbiome project 20220607 12GB Nucleotide
⇩ Human microbiome project 20220607 20GB Bisulfite
⇩ Human microbiome project (+ mm10 + hg19) 20220607 39GB Bisulfite
⇩ Fungi genomes 20220607 15GB Bisulfite

lambda2 branch (1.9.3 - 2.0.1)

  • Unpack the file after download with tar xf FILE.lambda.tar.gz. The resulting .lambda directory is the index.
  • Taxonomy information is included in some of the indexes, see Taxonomic Workflows for more information.
  • Memory usage during search is usually Unpacked Size + size-of-query-file ± 10%. The memory usage during the creation of the indexes was higher, around 2.5 * Unpacked Size.
Database Date Tax Download Size Unpacked Size
⇩ NR 20171205 79GB 151GB
⇩ Uniref100 20171205 75GB 137GB
⇩ Uniref90 20171205 40GB 64GB
⇩ Uniref50 20171205 16GB 25GB
⇩ Uniprot Trembl 20171205 54GB 98GB
⇩ Uniprot Sprot 20171205 0.3GB 0.7GB
Clone this wiki locally

AltStyle によって変換されたページ (->オリジナル) /