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shorten descriptions in example workflow
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AroneyS committed Dec 21, 2023
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Expand Up @@ -67,13 +67,15 @@ conda env config vars set CHECKM2DB="/checkm2/db/dir"
## Example workflow

```bash
# Assemble and recover from each sample individually with 20 samples used for differential abundance binning
# Assemble and recover from each sample individually
# 20 samples used for differential abundance binning
binchicken coassemble \
--forward-list samples_forward.txt --reverse-list samples_reverse.txt \
--run-aviary --single-assembly \
--cores 64 --output binchicken_single_assembly

# Assemble and recover from 2-sample coassemblies, prioritising samples with genomes not previously recovered
# Assemble and recover from 2-sample coassemblies
# Prioritising samples with genomes not previously recovered
binchicken iterate \
--coassemble-output binchicken_single_assembly \
--run-aviary --assemble-unmapped \
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