{"text_format":"2","workbook":"xlsx","n_sheets":1,"sheets":["Sheet1"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":0,"defined_names":0,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900"}

{"sheet":"Sheet1","index":0,"n_rows":67,"n_cols":18,"rows_kept":67,"cut":false,"hidden":false,"merged":[[2,11,3,11],[2,15,3,15],[2,10,3,10],[2,13,3,13],[2,14,3,14],[2,12,3,12],[2,17,3,17],[36,5,36,7],[60,0,60,12],[36,10,37,10],[36,3,36,4],[36,17,37,17],[36,1,36,2],[36,9,37,9],[36,8,37,8],[36,0,37,0],[21,9,22,9],[21,10,22,10],[21,17,22,17],[21,12,22,12],[21,13,22,13],[21,14,22,14],[21,8,22,8],[36,12,37,12],[36,11,37,11],[36,13,37,13],[36,14,37,14],[21,15,22,15],[36,15,37,15],[21,11,22,11],[21,1,21,2],[21,5,21,7],[21,3,21,4],[2,9,3,9],[2,0,3,0],[2,3,2,4],[2,1,2,2],[2,8,3,8],[21,0,22,0],[2,5,2,7]]}
[]
["HMP dataset"]
["Plasmid ID(RefSeq)","metaSPAdes",null,"Recycler",null,"metaplasmidSPAdes",null,null,"Coverage by k-mers","Length (bp)","Median host coverage by k-mers","Host","Dominant","Largest shared region with another plasmid of the same or larger coverage","Largest shared region with host (bp)"," Problem",null,"Coverage by reads"]
[null,"Genome fraction*, %","# contigs","Genome fraction, %","# contigs","Genome fraction, %","# contigs","Edges in assembly graph"]
["NC_005003.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,295.0,6585.0,39.0,"Staphylococcus epidermidis ATCC 12228","Yes","-","-",null,null,1295.022]
["NC_005004.1",99.992,3.0,99.992,1.0,99.992,1.0,6.0,216.0,24365.0,39.0,"Staphylococcus epidermidis ATCC 12228","Yes","-",3180.0,null,null,932.23]
["NC_005005.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,167.0,17261.0,39.0,"Staphylococcus epidermidis ATCC 12228","Yes","-","-",null,null,739.724]
["NC_005006.1",99.975,1.0,99.975,1.0,99.975,1.0,1.0,142.0,8007.0,39.0,"Staphylococcus epidermidis ATCC 12228","Yes","-","-",null,null,605.798]
["NC_005007.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,265.0,4679.0,39.0,"Staphylococcus epidermidis ATCC 12228","Yes","-","-",null,null,1124.534]
["NC_005008.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,732.0,4439.0,39.0,"Staphylococcus epidermidis ATCC 12228","Yes","-",1367.0,null,null,3264.118]
["NC_005707.1",99.536,9.0,"-","-","-","-",28.0,4.0,208369.0,1.9,"Bacillus cereus ATCC 10987 ","No","-",5934.0,"Repeat > 260",null,15.15]
["NC_007489.1",94.225,2.0,"-","-","-","-",12.0,44.0,105284.0,41.2,"Rhodobacter sphaeroides ATCC 17023","No","5122, NC_007490.2",1505.0,"Large common region with NC_007490.2 who has larger coverage",null,195.738]
["NC_007490.2",96.778,7.0,"-","-","-","-",23.0,71.0,100827.0,41.2,"Rhodobacter sphaeroides ATCC 17023","No","2490, NZ_CP015213.1",1832.0,"Repeat > 260",null,297.748]
["NC_009007.1",98.57,7.0,"-","-","-","-",24.0,67.0,114045.0,41.2,"Rhodobacter sphaeroides ATCC 17023","No","64255, NZ_CP015213.1",658.0,"Repeat > 260, 77% with NZ_CP015213.1",null,171.498]
["NZ_CP012966.1",93.59,3.0,"-","-","-","-",9.0,66.0,18815.0,41.2,"Rhodobacter sphaeroides ATCC 17023","No","17887, NC_009007.1","-","Repeat > 260, 98% with NC_009007.1",null,64.236]
["NZ_CP014442.1",100.0,2.0,"-","-",100.0,1.0,7.0,80.0,3125.0,39.0,"Staphylococcus epidermidis ATCC 12228","Yes","-","-","small (163bp) to NC_005007.1 ",null,392.89]
["NZ_CP015213.1",99.846,3.0,"-","-","-","-",22.0,83.0,124345.0,41.2,"Rhodobacter sphaeroides ATCC 17023","Yes","-",1607.0,"local coverage drop, long similar region with other rhodobacter plasmids",null,175.942]
["NZ_CP015215.1",100.0,2.0,"-","-","-","-",9.0,41.0,114095.0,41.2,"Rhodobacter sphaeroides ATCC 17023","No","1635, NZ_CP015213.1",1607.0,"long similar region with NZ_CP015213.1",null,184.022]
[]
[]
["MBARC dataset"]
["Plasmid ID(RefSeq)","metaSPAdes",null,"Recycler",null,"metaplasmidSPAdes",null,null,"Coverage by k-mers","Length (bp)","Median host coverage by k-mers","Host","Dominant","Largest shared region w/another plasmid  or same of larger coverage","Largest shared region w/host (bp)"," Problem",null,"Coverage by reads"]
[null,"Genome fraction, %","# of contigs","Genome fraction, %","# of contigs","Genome fraction, %","# of contigs","Edges in assembly graph"]
["NC_012983.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,155.0,84492.0,168.0,"Hirschia baltica ATCC 49814","Yes","-",0.0,null,null,1044.538]
["NC_014214.1",99.375,5.0,"-","-","-","-",22.0,108.0,124421.0,142.0,"Meiothermus silvanus DSM 9946","No","-",1252.0,"Repeat > 289",null,835.694]
["NC_018066.1",100.0,1.0,99.601,2.0,"-","-",null,786.0,60447.0,210.0,"Desulfosporosinus acidiphilus SJ4 ","Yes","-",0.0,"K127 - one linear contig, K55 - normal circular path. local coverage drop",null,5397.698]
["NC_018067.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,1837.0,3897.0,210.0,"Desulfosporosinus acidiphilus SJ4","Yes","-",0.0,null,null,12545.112]
["NC_019898.1",100.0,4.0,"-","-",100.0,1.0,15.0,263.0,149182.0,96.0,"Thermobacillus composti KWC4","Yes","-",3209.0,null,null,1807.456]
["NC_019937.1",99.154,1.0,98.864,1.0,100.0,1.0,1.0,80.0,12763.0,16.0,"Pseudomonas stutzeri RCH2","Yes","-",0.0,null,null,569.982]
["NC_019938.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,7.0,9865.0,16.0,"Pseudomonas stutzeri RCH2","Yes","-",0.0,null,null,51.856]
["NC_019939.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,343.0,2804.0,16.0,"Pseudomonas stutzeri RCH2","Yes","-",0.0,null,null,2643.254]
["NC_019975.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,263.0,12939.0,28.0,"Natronococcus occultus SP4","Yes","-",0.0,null,null,2193.086]
["NC_019976.1",100.0,3.0,"-","-","-","-",9.0,60.0,287963.0,28.0,"Natronococcus occultus SP4 ","No","-",1294.0,"Coverage close to chromosome NC_019974.1, shared regions larger than IS",null,288.406]
["NZ_CP011496.1 ",99.797,1.0,7.98,1.0,92.0,1.0,3.0,16.0,67545.0,2.7,"Escherichia coli strain NCM3722","Yes","-",0.0,"local coverage drop",null,105.72]
[]
["SYNTH dataset"]
["Plasmid ID(RefSeq)","metaSPAdes",null,"Recycler",null,"metaplasmidSPAdes",null,null,"Coverage by k-mers","Length (bp)","Median host coverage by k-mers","Host","Dominant","Largest shared region w/another plasmid  of same or larger coverage","Largest shared region w/host (bp)"," Problem",null,"Coverage by reads"]
[null,"Genome fraction, %","# of contigs","Genome fraction, %","# of contigs","Genome fraction, %","# of contigs","Edges in assembly graph"]
["NC_000959.1",97.495,7.0,"-","-","-","-",15.0,13.0,45704.0,3.3,"Deinococcus radiodurans R1 ","No","1070, NC_000958.1*",1208.0,"Repeat>206 repeat larger IS inside plasmid,  same coverage ~12 as NC_000958.1 (not found as reference because GF ~90 < 95%, large plasmid with gaps in coverage) shared large repeat\n",null,53.732]
["NC_001732.1",100.0,1.0,"-","-","-","-",2.0,12.91588,58407.0,16.0,"Methanocaldococcus jannaschii DSM 2661","No","-",1028.0,"issue with exSPAnder heuristics on tandem repeats! ",null,56.156]
["NC_001733.1",99.946,1.0,99.637,1.0,100.0,1.0,1.0,16.0,16550.0,16.0,"Methanocaldococcus jannaschii DSM 2661","Yes","-",0.0,null,null,59.792]
["NC_003240.1",99.782,3.0,"-","-","-","-",9.0,8.0,186614.0,6.2,"Nostoc sp. PCC 7120","No","1479, NC_003276.1",2387.0," low kmer coverage (7), simple repeat structure, shared region of length 1300 with NC_003267.1 (of coverage 5.)",null,32.522]
["NC_003241.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,16.0,5584.0,6.2,"Nostoc sp. PCC 7120","Yes","-",0.0,null,null,65.448]
["NC_003267.1",97.808,8.0,"-","-","-","-",24.0,5.24998,101965.0,6.2,"Nostoc sp. PCC 7120","No","1364, NC_003276.1",1369.0,"Repeat>206 - repeat larger IS inside plasmid; shared region of length 1300 with NC_003240.1",null,22.826]
["NC_003270.1",100.0,2.0,"-","-","-","-",6.0,8.0,40340.0,6.2,"Nostoc sp. PCC 7120","No","1868, NC_003273.1",1613.0," same coverage ~9 as NC_003273.1, shared large repeat\n",null,38.986]
["NC_003273.1",96.793,3.0,"-","-","-","-",23.0,11.0,55414.0,6.2,"Nostoc sp. PCC 7120","No","1686, NC_003276.1",741.0,"same coverage ~9 as NC_003270.1, shared large repeat\n",null,41.612]
["NC_003276.1",96.048,21.0,"-","-","-","-",60.0,38.0,408101.0,6.2,"Nostoc sp. PCC 7120","Yes","-",1432.0,"Repeat>206 - repeat larger IS inside plasmid; shared region of length 1300 with NC_003240.1",null,158.368]
["NC_004703.1",100.0,1.0,99.994,1.0,100.0,1.0,1.0,9.66368,33038.0,5.9,"Bacteroides thetaiotaomicron VPI-5482","Yes","-",0.0,null,null,42.016]
["NC_006462.1",96.998,24.0,2.89,1.0,"-","-",72.0,12.0,256992.0,12.0,"Thermus thermophilus HB8","No","1258, NC_017767.1",1262.0,"Repeat>206 - repeat larger IS inside plasmid",null,46.46]
["NC_006463.1",100.0,1.0,100.0,1.0,100.0,1.0,3.0,72.0,9322.0,12.0,"Thermus thermophilus HB8","Yes","-",1520.0,null,null,291.082]
["NC_009037.1",100.0,2.0,"-","-","-","-",6.0,5.0,16762.0,3.22,"Shewanella baltica OS185","No","-",13064.0,"coverage of some plasmid's parts < 5\n",null,24.644]
["NC_009136.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,91.0,8285.0,14.0,"Methanococcus maripaludis C5","Yes","-",0.0,null,null,386.83]
["NC_009661.1",92.26,30.0,"-","-","-","-",null,23.50876,83224.0,3.22,"Shewanella baltica OS185","No","presumably NC_0116651.1 10130, NC_011668.1 ",2591.0,"Repeat>206",null,102.212]
["NC_011668.1",94.47,16.0,"-","-",4.387,1.0,43.0,53.0,65448.0,2.89,"Shewanella baltica OS223","No","10130, NC_009661.1**",137.0," relatively low coverage, lots of shared regions with NC_011665.1 (not found as reference because genome fraction ~85 < 95%), complex case\n",null,76.76]
["NC_012036.1",100.0,5.0,"-","-",100.0,1.0,6.0,204.424,8291.0,8.0,"Caldicellulosiruptor bescii DSM 6725","Yes","-",2790.0,null,null,888.8]
["NC_012037.1",100.0,1.0,100.0,1.0,100.0,1.0,1.0,545.0,3653.0,8.0,"Caldicellulosiruptor bescii DSM 6725","Yes","-",0.0,null,null,2498.134]
["NC_012439.1",98.676,1.0,98.597,1.0,98.676,1.0,1.0,35.0,53682.0,17.0,"Persephonella marina EX-H1","Yes","-",0.0,"Repeat>206 - repeat larger IS inside plasmid",null,144.43]
["NC_013964.1",99.543,23.0,"-","-","-","-",null,6.0,437906.0,8.0,"Haloferax volcanii DS2 ","No","-",1403.0,"Repeat>206 - repeat larger IS inside plasmid",null,23.836]
["NC_017767.1",98.58,13.0,"-","-","-","-",null,15.0,81151.0,12.0,"Thermus thermophilus HB8","No","1258, NC_006462.1",1756.0," low coverage(10-15, as in chromosome), large repeat ~1000 inside",null,61.812]
[]
["Table S3: Benchmarking metaSPAdes, Recycler, and  metaplasmidSPAdes on HMP, MBARC, and SYNTH synthetic datasets The median k-mer coverage was computed based on the metaSPAdes assembly as described in Antipov et al, 2016. The genome fraction (%) is the percentage of the aligned bases in the reference genome. A base in the reference genome is aligned if there is a contig with an alignment to this base. A dominant plasmid in a metagenome is defined as a plasmid with coverage exceeding the coverage of chromosomes and other plasmids it share repeats with. The largest shared region was identified using MegaBLAST (Zhang, 2000). Plasmids NC_000958.1 and NC_009661.1 (with the median k-mer coverage 16x and 24x, respectively) were excluded from the plasmid reference set because their k-mer coverage drops to zero at some positions along their genomes."]
["*Plasmid NC_000958.1 has median k-mer coverage 16.1 but was excluded from reference set because of local coverage drops"]
["**Plasmid NC_009661.1 has median k-mer coverage 24.0 but was excluded from reference set because of local coverage drops"]
["Community composition:"]
["HMP - http://downloads.ihmpdcc.org/data/HMMC/HMPRP_sT1-Mock.pdf"]
["JGI - https://www.nature.com/articles/sdata201681/tables/1"]
["SYNTH - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665634/bin/NIHMS439897-supplement-Supp_Table_S1.xlsx"]