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Update Practical 5 Assembly and binning authored by Coto's avatar Coto
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Practical-5-Assembly-and-binning.md
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...@@ -34,18 +34,18 @@ Now we can run megahit as follows (**for the Illumina sample G**): ...@@ -34,18 +34,18 @@ Now we can run megahit as follows (**for the Illumina sample G**):
```plaintext ```plaintext
$ megahit -m 0.2 -1 G.1.fa -2 G.2.fa -o G-{your-assigned-kmer} -t 8 --min-contig-len 500 --k-list #your-assigned-kmer $ megahit -m 0.2 -1 G.1.fa -2 G.2.fa -o G-{your-assigned-kmer} -t 8 --min-contig-len 500 --k-list #your-assigned-kmer
``` ```
| Student | k-mer | `#` contigs (>500bp) | N50 and L50 | Longest contig (bp) | Total length (bp) | | Student | k-mer | `#` contigs (>500bp) | N50 | Longest contig (bp) | Total length (bp) |
|---------|-------|----------------------|-------------|---------------------|-------------------| |---------|-------|----------------------|------|---------------------|-------------------|
| | | | | | | | | | | | | |
| Leonard | 33 | | | | | | Leonard | 33 | 86,957 | 927 | 21,216 | 80.3M |
| | 37 | | | | | | | 37 | | | | |
| Louison | 43 | | | | | | Louison | 43 | 87,847 | 957 | 25,863 | 83M |
| Ava | 47 | | | | | | Ava | 47 | 86,670 | 960 | 32,943 | 82.5M |
| Ella | 53 | | | | | | Ella | 53 | | | | |
| Kinga | 57 | | | | | | Kinga | 57 | | | | |
| Nicole | 63 | | | | | | Nicole | 63 | 82,588 | 989 | 31,263 | 80M |
| Margret | 67 | | | | | | Margret | 67 | 18,719 | 910 | 10,407 | 17M |
| Mahum | 73 | | | | | | Mahum | 73 | 77,963 | 1,006 | 33,660 | 76M |
The assembly of samples using single k-mer sizes should take <span dir="">\~</span> 10 minutes. Once you have an assembly, you can use the stats.sh program from bbmap (/bioinf/software/bbmap) on the contigs file to get some basic information about it. The assembly of samples using single k-mer sizes should take <span dir="">\~</span> 10 minutes. Once you have an assembly, you can use the stats.sh program from bbmap (/bioinf/software/bbmap) on the contigs file to get some basic information about it.
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