The bacteria in Dataset A~C are downloaded from. ftp.ncbi.nih.gov/genomes/ ftp.ncbi.nih.gov/pub/taxonomy/ Read Length: 75bp Error Rate: 1% Insertion Distance: 250+-50bp The reads can be generated by Software MetaSim. First, we randomly generate 100 species from 18 genera and use them in Dataset A&C;then, we randomly picked 4 genera and picked 20 species from the list and use them in Dataset B. The list follows: Dataset A: Coverage Genome 1 Aliivibrio_salmonicida_LFI1238/NC_011312.fna 1 Vibrio_cholerae_M66_2/NC_012578.fna 1 Actinobacillus_pleuropneumoniae_L20/NC_009053.fna 1 Pasteurella_multocida/NC_002663.fna 1 Haemophilus_somnus_129PT/NC_008309.fna 1 Aggregatibacter_actinomycetemcomitans_D11S_1/NC_013416.fna 1 Mannheimia_succiniciproducens_MBEL55E/NC_006300.fna 1 Haemophilus_ducreyi_35000HP/NC_002940.fna 1 Comamonas_testosteroni_CNB_1/NC_013446.fna 1 Acidovorax_avenae_citrulli_AAC00-1/NC_008752.fna 1 Rhodoferax_ferrireducens_T118/NC_007908.fna 1 Variovorax_paradoxus_S110/NC_012791.fna 1 Polaromonas_JS666/NC_007948.fna 1 Delftia_acidovorans_SPH-1/NC_010002.fna 1 Verminephrobacter_eiseniae_EF01-2/NC_008786.fna 1 Acetobacter_pasteurianus_IFO_3283_01/NC_013209.fna 1 Gluconobacter_oxydans_621H/NC_006677.fna 1 Acidiphilium_cryptum_JF-5/NC_009484.fna 1 Gluconacetobacter_diazotrophicus_PAl_5_FAPERJ/NC_010125.fna 1 Granulobacter_bethesdensis_CGDNIH1/NC_008343.fna 2 Paracoccus_denitrificans_PD1222/NC_008686.fna 2 Rhodobacter_sphaeroides_2_4_1/NC_007493.fna 2 Roseobacter_denitrificans_OCh_114/NC_008209.fna 2 Ruegeria_pomeroyi_DSS_3/NC_003911.fna 2 Jannaschia_CCS1/NC_007802.fna 2 Clostridium_cellulolyticum_H10/NC_011898.fna 2 Haloarcula_marismortui_ATCC_43049/NC_006396.fna 2 Halobacterium_salinarum_R1/NC_010364.fna 2 Halorubrum_lacusprofundi_ATCC_49239/NC_012028.fna 2 Natrialba_magadii_ATCC_43099_uid46245/NC_013922.fna 2 Natronomonas_pharaonis/NC_007426.fna 2 Haloterrigena_turkmenica_DSM_5511_uid43501/NC_013743.fna 2 Halorhabdus_utahensis_DSM_12940/NC_013158.fna 2 Halomicrobium_mukohataei_DSM_12286/NC_013202.fna 2 Haloquadratum_walsbyi/NC_008212.fna 2 Bradyrhizobium_BTAi1/NC_009485.fna 2 Nitrobacter_hamburgensis_X14/NC_007964.fna 2 Rhodopseudomonas_palustris_BisA53/NC_008435.fna 2 Oligotropha_carboxidovorans_OM5/NC_011386.fna 2 Anaplasma_centrale_Israel/NC_013532.fna 3 Neorickettsia_risticii_Illinois/NC_013009.fna 3 Ehrlichia_canis_Jake/NC_007354.fna 3 Anaplasma_phagocytophilum_HZ/NC_007797.fna 3 Orientia_tsutsugamushi_Boryong/NC_009488.fna 3 Rickettsia_africae_ESF_5/NC_012633.fna 3 Rickettsia_canadensis_McKiel/NC_009879.fna 3 Rickettsia_bellii_OSU_85-389/NC_009883.fna 3 Thermotoga_lettingae_TMO/NC_009828.fna 3 Thermosipho_africanus_TCF52B/NC_011653.fna 3 Fervidobacterium_nodosum_Rt17-B1/NC_009718.fna 3 Petrotoga_mobilis_SJ95/NC_010003.fna 3 Kosmotoga_olearia_TBF_19_5_1/NC_012785.fna 3 Streptococcus_agalactiae_2603/NC_004116.fna 3 Lactococcus_lactis_cremoris_MG1363/NC_009004.fna 3 Streptococcus_dysgalactiae_equisimilis_GGS_124/NC_012891.fna 3 Desulfotomaculum_acetoxidans_DSM_771/NC_013216.fna 3 Desulfitobacterium_hafniense_DCB_2/NC_011830.fna 3 Pelotomaculum_thermopropionicum_SI/NC_009454.fna 3 Candidatus_Desulforudis_audaxviator_MP104C/NC_010424.fna 3 Fusobacterium_nucleatum/NC_003454.fna 4 Leptotrichia_buccalis_DSM_1135/NC_013192.fna 4 Sebaldella_termitidis_ATCC_33386/NC_013517.fna 4 Streptobacillus_moniliformis_DSM_12112/NC_013515.fna 4 Atopobium_parvulum_DSM_20469/NC_013203.fna 4 Slackia_heliotrinireducens_DSM_20476/NC_013165.fna 4 Eggerthella_lenta_DSM_2243/NC_013204.fna 4 Cryptobacterium_curtum_DSM_15641/NC_013170.fna 4 Microcystis_aeruginosa_NIES_843/NC_010296.fna 4 Cyanobacteria_bacterium_Yellowstone_A-Prime/NC_007775.fna 4 Synechocystis_PCC6803/NC_000911.fna 4 Cyanothece_ATCC_51142/NC_010546.fna 4 Thermosynechococcus_elongatus/NC_004113.fna 4 Azoarcus_BH72/NC_008702.fna 4 Thauera_MZ1T/NC_011662.fna 4 Dechloromonas_aromatica_RCB/NC_007298.fna 4 Aromatoleum_aromaticum_EbN1/NC_006513.fna 4 Cellvibrio_japonicus_Ueda107/NC_010995.fna 4 Pseudomonas_entomophila_L48/NC_008027.fna 4 Pseudomonas_aeruginosa_LESB58/NC_011770.fna 4 Pseudomonas_fluorescens_Pf0_1/NC_007492.fna 5 Pseudomonas_putida_F1/NC_009512.fna 5 Pseudomonas_syringae_tomato_DC3000/NC_004578.fna 5 Pseudomonas_syringae_pv_B728a/NC_007005.fna 5 Pseudomonas_syringae_phaseolicola_1448A/NC_005773.fna 5 Pseudomonas_stutzeri_A1501/NC_009434.fna 11 Lysinibacillus_sphaericus_C3_41/NC_010382.fna 12 Oceanobacillus_iheyensis/NC_004193.fna 13 Geobacillus_kaustophilus_HTA426/NC_006510.fna 14 Anoxybacillus_flavithermus_WK1/NC_011567.fna 15 Bacillus_clausii_KSM-K16/NC_006582.fna 16 Bacillus_anthracis_A0248/NC_012659.fna 17 Bacillus_amyloliquefaciens_FZB42/NC_009725.fna 18 Ralstonia_pickettii_12D/NC_012856.fna 19 Cupriavidus_taiwanensis/NC_010528.fna 20 Burkholderia_mallei_ATCC_23344/NC_006348.fna 21 Burkholderia_glumae_BGR1/NC_012721.fna 22 Polynucleobacter_necessarius_asymbioticus_QLW_P1DMWA_1/NC_009379.fna 23 Burkholderia_383/NC_007509.fna 24 Photobacterium_profundum_SS9/NC_006370.fna 25 Vibrio_harveyi_ATCC_BAA-1116/NC_009783.fna Dataset B: Coverage Genome 1 Lysinibacillus_sphaericus_C3_41/NC_010382.fna 2 Oceanobacillus_iheyensis/NC_004193.fna 3 Geobacillus_kaustophilus_HTA426/NC_006510.fna 4 Anoxybacillus_flavithermus_WK1/NC_011567.fna 5 Bacillus_clausii_KSM-K16/NC_006582.fna 6 Bacillus_anthracis_A0248/NC_012659.fna 7 Bacillus_amyloliquefaciens_FZB42/NC_009725.fna 8 Ralstonia_pickettii_12D/NC_012856.fna 9 Cupriavidus_taiwanensis/NC_010528.fna 10 Burkholderia_mallei_ATCC_23344/NC_006348.fna 11 Burkholderia_glumae_BGR1/NC_012721.fna 12 Polynucleobacter_necessarius_asymbioticus_QLW_P1DMWA_1/NC_009379.fna 13 Burkholderia_383/NC_007509.fna 14 Photobacterium_profundum_SS9/NC_006370.fna 15 Vibrio_harveyi_ATCC_BAA-1116/NC_009783.fna 16 Aliivibrio_salmonicida_LFI1238/NC_011312.fna 17 Vibrio_cholerae_M66_2/NC_012578.fna 18 Actinobacillus_pleuropneumoniae_L20/NC_009053.fna 19 Pasteurella_multocida/NC_002663.fna 20 Haemophilus_somnus_129PT/NC_008309.fna Dataset C: Coverage Genome 1 Aggregatibacter_actinomycetemcomitans_D11S_1/NC_013416.fna 1 Mannheimia_succiniciproducens_MBEL55E/NC_006300.fna 1 Haemophilus_ducreyi_35000HP/NC_002940.fna 1 Comamonas_testosteroni_CNB_1/NC_013446.fna 1 Acidovorax_avenae_citrulli_AAC00-1/NC_008752.fna 1 Rhodoferax_ferrireducens_T118/NC_007908.fna 1 Variovorax_paradoxus_S110/NC_012791.fna 1 Polaromonas_JS666/NC_007948.fna 1 Delftia_acidovorans_SPH-1/NC_010002.fna 1 Verminephrobacter_eiseniae_EF01-2/NC_008786.fna 1 Acetobacter_pasteurianus_IFO_3283_01/NC_013209.fna 1 Gluconobacter_oxydans_621H/NC_006677.fna 1 Acidiphilium_cryptum_JF-5/NC_009484.fna 1 Gluconacetobacter_diazotrophicus_PAl_5_FAPERJ/NC_010125.fna 1 Granulobacter_bethesdensis_CGDNIH1/NC_008343.fna 1 Paracoccus_denitrificans_PD1222/NC_008686.fna 1 Rhodobacter_sphaeroides_2_4_1/NC_007493.fna 1 Roseobacter_denitrificans_OCh_114/NC_008209.fna 1 Ruegeria_pomeroyi_DSS_3/NC_003911.fna 1 Jannaschia_CCS1/NC_007802.fna 2 Clostridium_cellulolyticum_H10/NC_011898.fna 2 Haloarcula_marismortui_ATCC_43049/NC_006396.fna 2 Halobacterium_salinarum_R1/NC_010364.fna 2 Halorubrum_lacusprofundi_ATCC_49239/NC_012028.fna 2 Natrialba_magadii_ATCC_43099_uid46245/NC_013922.fna 2 Natronomonas_pharaonis/NC_007426.fna 2 Haloterrigena_turkmenica_DSM_5511_uid43501/NC_013743.fna 2 Halorhabdus_utahensis_DSM_12940/NC_013158.fna 2 Halomicrobium_mukohataei_DSM_12286/NC_013202.fna 2 Haloquadratum_walsbyi/NC_008212.fna 2 Bradyrhizobium_BTAi1/NC_009485.fna 2 Nitrobacter_hamburgensis_X14/NC_007964.fna 2 Rhodopseudomonas_palustris_BisA53/NC_008435.fna 2 Oligotropha_carboxidovorans_OM5/NC_011386.fna 2 Anaplasma_centrale_Israel/NC_013532.fna 2 Neorickettsia_risticii_Illinois/NC_013009.fna 2 Ehrlichia_canis_Jake/NC_007354.fna 2 Anaplasma_phagocytophilum_HZ/NC_007797.fna 2 Orientia_tsutsugamushi_Boryong/NC_009488.fna 2 Rickettsia_africae_ESF_5/NC_012633.fna 3 Rickettsia_canadensis_McKiel/NC_009879.fna 3 Rickettsia_bellii_OSU_85-389/NC_009883.fna 3 Thermotoga_lettingae_TMO/NC_009828.fna 3 Thermosipho_africanus_TCF52B/NC_011653.fna 3 Fervidobacterium_nodosum_Rt17-B1/NC_009718.fna 3 Petrotoga_mobilis_SJ95/NC_010003.fna 3 Kosmotoga_olearia_TBF_19_5_1/NC_012785.fna 3 Streptococcus_agalactiae_2603/NC_004116.fna 3 Lactococcus_lactis_cremoris_MG1363/NC_009004.fna 3 Streptococcus_dysgalactiae_equisimilis_GGS_124/NC_012891.fna 3 Desulfotomaculum_acetoxidans_DSM_771/NC_013216.fna 3 Desulfitobacterium_hafniense_DCB_2/NC_011830.fna 3 Pelotomaculum_thermopropionicum_SI/NC_009454.fna 3 Candidatus_Desulforudis_audaxviator_MP104C/NC_010424.fna 3 Fusobacterium_nucleatum/NC_003454.fna 3 Leptotrichia_buccalis_DSM_1135/NC_013192.fna 3 Sebaldella_termitidis_ATCC_33386/NC_013517.fna 3 Streptobacillus_moniliformis_DSM_12112/NC_013515.fna 3 Atopobium_parvulum_DSM_20469/NC_013203.fna 3 Slackia_heliotrinireducens_DSM_20476/NC_013165.fna 4 Eggerthella_lenta_DSM_2243/NC_013204.fna 4 Cryptobacterium_curtum_DSM_15641/NC_013170.fna 4 Microcystis_aeruginosa_NIES_843/NC_010296.fna 4 Cyanobacteria_bacterium_Yellowstone_A-Prime/NC_007775.fna 4 Synechocystis_PCC6803/NC_000911.fna 4 Cyanothece_ATCC_51142/NC_010546.fna 4 Thermosynechococcus_elongatus/NC_004113.fna 4 Azoarcus_BH72/NC_008702.fna 4 Thauera_MZ1T/NC_011662.fna 4 Dechloromonas_aromatica_RCB/NC_007298.fna 4 Aromatoleum_aromaticum_EbN1/NC_006513.fna 4 Cellvibrio_japonicus_Ueda107/NC_010995.fna 4 Pseudomonas_entomophila_L48/NC_008027.fna 4 Pseudomonas_aeruginosa_LESB58/NC_011770.fna 4 Pseudomonas_fluorescens_Pf0_1/NC_007492.fna 4 Pseudomonas_putida_F1/NC_009512.fna 4 Pseudomonas_syringae_tomato_DC3000/NC_004578.fna 4 Pseudomonas_syringae_pv_B728a/NC_007005.fna 4 Pseudomonas_syringae_phaseolicola_1448A/NC_005773.fna 4 Pseudomonas_stutzeri_A1501/NC_009434.fna 6 Lysinibacillus_sphaericus_C3_41/NC_010382.fna 7 Oceanobacillus_iheyensis/NC_004193.fna 8 Geobacillus_kaustophilus_HTA426/NC_006510.fna 9 Anoxybacillus_flavithermus_WK1/NC_011567.fna 10 Bacillus_clausii_KSM-K16/NC_006582.fna 11 Bacillus_anthracis_A0248/NC_012659.fna 12 Bacillus_amyloliquefaciens_FZB42/NC_009725.fna 13 Ralstonia_pickettii_12D/NC_012856.fna 14 Cupriavidus_taiwanensis/NC_010528.fna 15 Burkholderia_mallei_ATCC_23344/NC_006348.fna 16 Burkholderia_glumae_BGR1/NC_012721.fna 17 Polynucleobacter_necessarius_asymbioticus_QLW_P1DMWA_1/NC_009379.fna 18 Burkholderia_383/NC_007509.fna 19 Photobacterium_profundum_SS9/NC_006370.fna 20 Vibrio_harveyi_ATCC_BAA-1116/NC_009783.fna 21 Aliivibrio_salmonicida_LFI1238/NC_011312.fna 22 Vibrio_cholerae_M66_2/NC_012578.fna 23 Actinobacillus_pleuropneumoniae_L20/NC_009053.fna 24 Pasteurella_multocida/NC_002663.fna 25 Haemophilus_somnus_129PT/NC_008309.fna Real data is downloaded from: gutmeta.genomics.org.cn