Table 1 CheckM1 evaluation of binning algorithms. The second column shows the \(N_d\) diversities estimated by Nonpareil [27], which is empirically correlated with alpha diversity. The third column shows the number of circular near-complete contigs, near-complete contigs (\(\ge 90\%\) completeness and \(<5\%\) contamination), and high-quality contigs (\(\ge 70\%\) completeness and \(<10\%\) contamination) before binning. The three numbers in each following cell give the number of near-complete MAGs, high-quality MAGs, and medium-quality MAGs, respectively. In the table, “raw“ stands for raw output by the binning algorithm; “+post” for post-processing by putting \(\ge 1\)Mb circular contigs into separate bins; “+rescue” for merging with circular paths rescued based on the graph topology. Column “All” shows the count of near-complete MAGs in a union of all binners (deduplicated at 1% mash distance), and column “hmBin unique” shows the count of near-complete MAGs SemiBin1 was run in the long-read mode and GraphMB was run without knowledge of single-copy marker genes

chicken-gut-1

18.29

74|78|17

93|21|18

81|27|16

90|32|16

92|30|16

88|24|16

81|15|14

95|40|27

99

1

env-digester-1

18.98

20|22|14

33|20|19

23|16|16

27|19|15

35|21|18

32|21|17

34|24|19

35|34|25

38

8

env-digester-2

18.59

29|38|27

55|23|24

34|30|28

44|31|29

58|35|31

50|40|27

52|38|29

58|62|47

62

14

env-digester-3

18.31

39|47|21

67|38|32

48|40|31

53|42|33

71|44|35

70|46|36

69|43|38

76|72|52

76

17

env-digester-4

18.57

44|58|25

85|29|29

58|38|29

68|37|31

87|34|33

79|33|22

81|28|28

95|58|43

100

17

env-hotspring-1

18.45

16|19|11

33|14|14

18|22|13

24|21|14

34|21|14

33|19|18

33|16|15

35|28|21

37

10

human-gut-1

19.20

51|68|30

80|29|18

64|35|25

83|41|28

87|41|29

79|36|20

79|37|19

93|61|64

104

4

human-gut-10

18.44

25|34|14

39|18|16

40|23|22

44|24|22

44|24|24

40|17|20

38|17|18

42|31|32

50

2

human-gut-2

19.17

59|73|34

84|34|24

66|41|30

85|47|32

93|48|32

84|44|42

84|41|41

94|69|73

103

5

human-gut-3

17.31

42|49|1

52|4|9

45|10|12

51|10|12

51|10|12

53|9|7

51|9|6

53|12|13

56

0

human-gut-4

19.00

19|25|9

33|18|13

38|29|33

38|31|33

38|30|31

34|27|26

38|22|25

42|39|36

48

0

human-gut-5

18.53

7|10|12

19|8|7

18|9|10

19|11|11

22|10|11

19|16|9

15|13|12

23|17|19

24

2

human-gut-6

16.99

7|11|4

14|7|7

15|14|9

15|14|9

15|13|9

13|7|6

13|8|6

17|12|10

18

0

human-gut-7

18.51

17|22|14

24|15|13

25|21|20

26|22|21

27|22|21

22|19|14

24|17|15

26|30|22

28

0

human-gut-8

17.75

3|6|3

11|8|3

19|13|15

19|13|15

18|13|15

7|8|10

8|5|10

15|15|19

22

0

human-gut-9

17.87

12|15|7

25|5|5

22|13|20

23|13|21

24|13|21

24|12|15

22|9|19

29|10|14

30

0

sheep-gut-1a

19.44

144|186|40

189|53|28

147|52|30

193|62|32

204|60|30

188|56|31

189|50|32

212|80|57

217

9

sheep-gut-1b

19.53

317|423|100

417|131|82

345|116|94

450|134|100

466|136|96

414|130|75

403|109|56

490|211|167

509

7

unk-unk-1

19.17

25|28|12

34|21|11

25|20|16

30|20|17

36|23|18

37|24|16

37|25|17

40|36|21

41

7