Main tool : Shovill
Additional tools:
- bwa 0.7.19
- kmc 3.2.4
- lighter 1.1.3
- megahit 1.2.9
- perl 5.34.0
- pilon 1.24
- python 3.10.42
- samclip 0.4.0
- samtools 1.16.1
- seqkit 2.12.0
- SKESA and gfa_connector 2.5.0
- SPAdes 3.15.5
- trimmomatic 0.40
- velvet 1.2.10
Full documentation: https://github.com/tseemann/shovill
Assemble bacterial isolate genomes from Illumina paired-end reads
# run shovill on the test FASTQ files bundled with shovill
shovill --outdir /data/out.spades --assembler spades --R1 /shovill-1.1.0/test/R1.fq.gz --R2 /shovill-1.1.0/test/R2.fq.gz