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change demo samples
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previous ones had few targets for single-sample
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AroneyS committed Jan 10, 2025
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Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions docs/demo.md
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Expand Up @@ -11,7 +11,7 @@ Download 4 SRA samples and run single-sample assembly with co-binning.

```bash
binchicken single \
--forward SRR8334323 SRR8334324 SRR6797127 SRR6797128 --sra \
--forward SRR14271365 SRR14271372 ERR2281802 ERR2281803 --sra \
--cores 16 --output binchicken_single_assembly
```

Expand All @@ -23,7 +23,7 @@ This will produce metagenome-assembled genomes (MAGs) from each sample.

```bash
binchicken single \
--forward SRR8334323 SRR8334324 SRR6797127 SRR6797128 --sra \
--forward SRR14271365 SRR14271372 ERR2281802 ERR2281803 --sra \
--run-aviary --cores 64 --output binchicken_single_assembly
```

Expand All @@ -47,16 +47,16 @@ binchicken iterate \
--run-aviary --cores 64 --output binchicken_3_coassembly
```

As you might expect from checking the sample sources (e.g. [SRR8334323](https://sandpiper.qut.edu.au/run/SRR8334323)),
the SRR8334323/SRR8334324 and SRR6797127/SRR6797128 pairs are suggested for coassembly.
As you might expect from checking the sample sources (e.g. [SRR14271365](https://sandpiper.qut.edu.au/run/SRR14271365)),
the SRR14271365/SRR14271372 and ERR2281802/ERR2281803 pairs are suggested for coassembly.

## Coassembly with co-binning

Alternatively, you can start with coassembly, optionally providing your own genomes.

```bash
binchicken coassemble \
--forward SRR8334323 SRR8334324 SRR6797127 SRR6797128 --sra \
--forward SRR14271365 SRR14271372 ERR2281802 ERR2281803 --sra \
--genomes-list genomes.txt \
--run-aviary --cores 64 --output binchicken_coassembly
```
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