A systematic comparison of chloroplast genome assembly tools

Table 4 Tools and version information used in our benchmark setup

Tool	Source Repository	Commit used for benchmarking
GetOrganelle	https://github.com/Kinggerm/GetOrganelle.git	587c1c51c34e270eb9178a42a77a5150157e6925
IOGA	https://github.com/holmrenser/IOGA.git	c460ea9d9fe176fec2bd76d369b0cbb36793b2bf
NOVOPlasty	https://github.com/ndierckx/NOVOPlasty.git	6af0894f8ea1d76a1b71df9cb762cf6e48dceac1
chloroExtractor	https://github.com/chloroExtractorTeam/chloroExtractor.git	87364e48ec84a3f6ee91fc8d995b0bda5a0fa82d
Chloroplast assembly protocol	https://github.com/eead-csic-compbio/chloroplast_assembly_protocol.git	250d16ac02005d6a5939bf182b3d2995d0e88229
Fast-Plast	https://github.com/mrmckain/Fast-Plast.git	7e32b2e797fd1f49d32d6559e8345afefbaff803
ORG.Asm	https://git.metabarcoding.org/org-asm/org-asm.git	830313acae3ca773b63f6bea9fc6d017e021bde5

All tools are wrapped into docker containers and stored on dockerhub [55]. The corresponding tags and SHA256 checksums are reported in Additional file 1: Table S3

ISSN: 1474-760X