Science Advances

Supplementary Materials

This PDF file includes:

  • fig. S1. Generation of raw CCs.
  • fig. S2. Iterative Louvain procedure and characterization of CCs.
  • fig. S3. Comparison of CAGs and meta3C approaches.
  • fig. S4. Scaffolding of dozens of bacterial chromosomes.
  • fig. S5. Example of post-GRAAL scaffold correction.
  • fig. S6. Structural behavior of phage SPβ in B. subtilis genome.
  • fig. S7. Schematic representation of the phiKZ-like genome.
  • fig. S8. Interactions of phages with bacterial genomes.
  • fig. S9. CRISPR spacers’ blast output.
  • Legends for tables S1 to S4
  • data set S1. Contig data (contigs_id, contig_name, GC content, coverage, core_community_index, core_size).
  • data set S2. Normalized contig network (contig_1, contig_2, normalized interaction).
  • data set S3. This file contains all the GRAAL scaffolds larger than 300 kb (FASTA format).
  • data set S4. This file, in complement of data set S3, contains all the contigs not included in the scaffolds larger than 300 kb (FASTA format).
  • data set S5. This file contains all the CC assemblies (contigs >5 kb, FASTA format) that were not scaffolded by GRAAL because of their small size (cumulated size, <500 kb; see steps 4 and 5 in fig. S2).

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Other Supplementary Material for this manuscript includes the following:

  • table S1 (Microsoft Excel format). Description of the 140 largest genomic structures (>500 kb) detected in the mice gut microbiome and their assembly/scaffolding statistics.
  • table S2 (Microsoft Excel format). Description of the 59 contigs corresponding to candidate phages hailing from the unscaffolded output of the GRAAL software.
  • table S3 (Microsoft Excel format). Description of the 43 contigs hailing from the reassembly of small CCs and corresponding to candidate phages.
  • table S4 (Microsoft Excel format). CRISPR spacers’ blast output (format #6).

Files in this Data Supplement: