diff --git a/docs/preprocess.md b/docs/preprocess.md index 3e526f7..59a56fb 100644 --- a/docs/preprocess.md +++ b/docs/preprocess.md @@ -88,3 +88,16 @@ edge_5,2 ### Before using Flye assemblies for binning Before using Flye assemblies for binning, please use [`gfa2fasta`](https://github.com/Vini2/GraphBin2/blob/master/src/graphbin2/support/gfa2fasta.py) command to get the edge sequences. Further details can be found [here](https://github.com/Vini2/GraphBin2/blob/master/src/graphbin2/support/README.md#gfa2fastapy). More details can be found in the next page. + +## Obtain the coverage of contigs (`abundance.tsv`) + +You can use [CoverM](https://github.com/wwood/CoverM) to get the coverage of contigs. You can run the following commands to get the `abundance.tsv` file. Please make sure that there are **no headers** in the `abundance.tsv` file. + +``` +coverm contig -1 reads_1.fastq -2 reads_2.fastq -r contigs.fasta -o abundance.tsv -t 8 +sed -i '1d' abundance.tsv # remove the header of the file +``` + +The resulting `abundance.tsv` file can be directly used in GraphBin2. + +Once you have obtained the assembly output, binning results and the coverage information file, you can run GraphBin2. \ No newline at end of file