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IDs: 890181 [UID] 3727208 [GenBank] 3768438 [RefSeq]
Sequencing was done with Illumina HiSeq 2500 paired-ends and Illumina HiSeq 2500 mate-paired. This assembly was constructed with CutAdapt (min length 25 bp, rounds 3, match length 5 bp) v. 1.1; FLASH (mate-paired 3' overlap read pairs discarded) v. ... 1.2.2; Kmerfreq v. 2015-05-28; SOAPdenovo2 (PE only) v. 2015-05-28; SSPACE2 (5 rounds per library insert size, ascending size order) v. 2.0; BGI GapCloser (5 rounds, PE libraries only) v. 2015-05-28 and 100kb BAC-end scaffolding - Bambus (range 50-400,000) v. 2015-05-28. Gaps of unknown size >10 bp were converted to 100bp, Repeatmasker(-no _is -norna -noint) and Tandem Repeats Finder (2 7 7 80 10 50 50 -f -d -m -h) were run, and then sequences were discarded if they were < 200 bp length OR >= 50% repetitive, simple repeat or unknown N bases. LG mapping was done via ePCR (<=2gap, <=2mis, amplicon 10-1000bp(Fluidigm) 10-5000bp(other)) and Glycine max synteny: MUMmer (promer --mum --filter, >=90% sim). more
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