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Assesing Transscript Abundance

Software Options

kallisto quantifies abundances of transcripts from RNA-Seq data, or more other target sequences using high-throughput sequencing reads. Modules on Mogon can be found as1):


sleuth investigates RNA-Seq transcript abundance from kallisto and perform differential expression analysis. Modules on Mogon can be found as:


Development with SeqAn3

SeqAn3 is C++ library for sequence analysis. It is a follow-up project of SeqAn2 and strives to implement efficient algorithms as a header-only library.

It provides broad functionality, can be used together with OpenMP, even MPI and relatively easy to use2).

The module for SeqAn3 is located at


The older module for SeqAn23) can still be found at:


For version 3.0.0 the following aspects apply

  • The API is not stable, yet4).
  • Loading the module will load a recent GCC and CMake.

If using CMake, be sure to include the following statements5)

set(SeqAn3_DIR "$ENV{EBROOTSEQAN}/build_system")
find_package (SeqAn3 REQUIRED)

loading a module without version specification will load the most recent one
provided you “speak” C++.
assorted in devel because it is not only a library
Presumably because the new libraries are not yet ships with STL. W.a.W.: Using the library, developing applications will likely need an adaption of include-statements, but little more.
In contrast, the tutorial assumes set(SeqAn3_DIR “${CMAKE_SOURCE_DIR}/../seqan3/build_system.
  • start/software/topical/lifesciences/ngs/transcript_abundance_tools.1587044008.txt.gz
  • Last modified: 2020/04/16 15:33
  • by jrutte02