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Assesing Transscript Abundance
Software Options
kallisto
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):
bio/kallisto
sleuth
sleuth investigates RNA-Seq transcript abundance from kallisto and perform differential expression analysis. Modules on Mogon can be found as:
bio/sleuth
Development with SeqAn3
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).
Using the Module
The module for SeqAn3 is located at
lib/seqan/<version>
The older module for SeqAn23) can still be found at:
devel/seqan/2.4.0
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)
devel
because it is not only a library