RAPT¶

Description¶

RAPT is an NCBI pipeline designed for assembling and annotating short genomic sequencing reads obtained from bacterial or archaeal isolates de novo. It takes an SRA run or a fasta or fastq file of Illumina reads as input and produces an assembled and annotated genome of quality comparable to RefSeq in a couple of hours. RAPT consists of three major components, the genome assembler SKESA, the taxonomic assignment tool ANI and the Prokaryotic Genome Annotation Pipeline (PGAP). Use the RC wrapper "run_rapt" instead of the original "run_rapt.py" script.

Environment Modules¶

Run module spider rapt to find out what environment modules are available for this application.

Environment Variables¶

HPC_RAPT_DIR - installation directory
HPC_RAPT_BIN - executable directory
HPC_RAPT_IMAGE - container image path

Categories¶

biology,assembly