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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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question with reassemble_bins module #291

Open xushaoyi opened 4 years ago

xushaoyi commented 4 years ago

**dear author, sorry to disturb you, but it seems something wrong with the reassemble_bin module. when I use the pipeline, finally i got the result but, the contamination of reassembled bins (bin.strict and bin,permissive) were very high. did it a normal phenomenon? the command is: metawrap reassemble_bins -o temp/binning/cmx_reassembly_bin8_1 -1 seq/6sample_1.fq -2 seq/6sample_2.fq -t 96 -m 100 -c 70 -x 10 -b temp/binning/cmx_bins/bin_8/

the out put is as follows: image

ursky commented 4 years ago

This is normal. If an organism has other closely related speicies in the sample the reads pulled for reassembly will introduce too much extra contamination and the reassembly will ruin the bin. Typically only some of the bins in a sample will be improved by the reassembly, which is why the pipeline falls back on the original ("orig") bin if the metrics are not improved.

xushaoyi commented 4 years ago

This is normal. If an organism has other closely related speicies in the sample the reads pulled for reassembly will introduce too much extra contamination and the reassembly will ruin the bin. Typically only some of the bins in a sample will be improved by the reassembly, which is why the pipeline falls back on the original ("orig") bin if the metrics are not improved.

oh，thanks！