SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity. If desired, SKESA contigs could be connected into a GFA graph using GFA connector.
SAUTE is a de Bruijn graph based target enriched de-novo assembler designed for assembling genomic and RNA-seq reads sequenced using Illumina. The result is reported as a GFA graph and two nucleotide fasta sequence files for assemblies in the graph.
See which versions are available:
$ module avail skesa
Load one version into your environment and run it:
$ module load skesa/2.5.1 $ skesa
Notes from the sysadmin during installation:
$ cd /tmp $ git clone https://github.com/ncbi/SKESA.git -b skesa.2.4.0_saute.1.3.0_2 $ cd SKESA $ sudo dnf install boost-static $ make $ sudo mkdir -p /export/apps/skesa/2.5.1/bin $ sudo cp gfa_connector kmercounter saute saute_prot skesa /export/apps/skesa/2.5.1/bin
Note: the git tag doesn't always match the version, see: https://github.com/ncbi/SKESA/blob/skesa.2.4.0_saute.1.3.0_2/skesa.cpp