lambda2 guide

This guide covers the most important differences between lambda1 (0.9 - 1.1) and lambda2 (1.9 - 2.0.1).

Command line interface (general) (since 1.9.4)

Lambda1 had two executables: lambda and lambda_indexer
Lambda2 has a single executable: lambda2

lambda2 has different sub-commands, similar to git. Currently the following are supported

• mkindexn Index creation, similar to lambda_indexer -p blastn previously
• mkindexp Index creation, similar to lambda_indexer with any other -p previously
• searchn The actual search, similar to lambda -p blastn previously
• searchp The actual search, similar to lambda with any other -p previously

Some options have disappeared, e.g. -p/--program and for some options the short notation disappeared or has been renamed so that all short options are now single-letter.

Databases and Indexes

1. Lambda now stores its index files in a separate folder instead of cluttering the directory where your original .fasta file was. These folders have a .lambda extension, but are regular folders that just contain the different data files needed. This means it is also easy to create different index folders from the same original .fasta file.

2. The option has been renamed from -d to -i! This is because -d is still the option for the input of the lambda_indexer.

3. Support for Masking has been removed. It didn't improve the results; there is variable length seeding to handle repetitive regions.

Taxonomic workflows

Lambda now supports multiple options that assist you when working with (or searching for) taxonomies. Please see the extra article.

Output-Formats

New optional tags were added to SAM/BAM, but also some old tags were renamed, see SAMTOOLS Output Formats.