This pipeline was used for raw sequence quailty control, metagenome assembly, binning of metagenome-assembled genomes (MAGs), detection of structural variations and and dynamic methylomes based on the NGS and nanopore sequencing data.
This pipeline was described in the following publication: Short- and long-read metagenomics expand individualized structural variations in gut microbiomes https://www.nature.com/articles/s41467-022-30857-9
ONT and Illumina sequencing data generated from this study is deposited at National Microbiology Data Center (https://nmdc.cn/) with accession number of NMDC10017965.
MetaWRAP 1.2
Guppy v.3.3.0
minimap2 v2.17-r941
Canu 1.7
Flye 2.8.1-b1676
OPERA-MS v0.9.0
Spades v3.13.0
fastANI 1.32
MUM&Co v2.4.2
IGV 2.6.2
Prokka 1.13
emapper.py 1.0.3
seqkit v0.10.2
dRep v2.6.2
gtdbtk 1.3.0
RNammer -1.2
samtools 0.13.0
ProphageHunter
CD-hit v4.7
MAFFT v7.450
CAT
IQTREE2
iTOL v5
CRSPRDetect v2.4
blast v2.6.0
Tombo v1.5.1
Nanopolish v0.11.1
mCaller v0.3
Nanodisco v1.0.0
These software could be installed by conda.
0_Zymo_community_standard_data_assembly.sh
This pipeline was used for evaluation of assembly quality of Canu 1.7, Flye 2.8.1-b1676, OPERA-MS and Spades based on Zymo_community_Standards_data.
0_1_self_quant_bins.sh
One script was used for the estimation of abundance of MAGs based on the NGS reads.
1_Gut_metagenome_assembly&binning.sh
Part I read quality control, hybird assembly, binning of contigs, dreplication and classficatio of MAG.
2_Gut_metagenome_SV_analysis.sh
Part II Structure detection of MAGs and related genes prediction and annotation.
3_Prophage_prediction.sh
Part III. Prediction of prophage, redundancy removal, gene annotation, and construction of evolutionary trees.
4_CRISPR_spacers_prediction.sh
Part IV. Predicting CRISPR spacers from the contigs of all samples
5_Methylation.sh
Part V. Determination of DNA methylation using tombo software in genomes with more than 10 samples present.
Directory: metadata
This directory include the matadata of this experiment and some useful intermediate file.