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metagenome2
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gbouras13 committed Jun 2, 2023
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##### Metagenomics
# Metagenomics

As it currently stands, we do not recommend `plassembler` for metagenomic sequences. This is because of their high diversity, leading to difficulties in recovering chromosome-length contigs for bacteria. Additionally, Unicycler (a core dependency of Plassembler) is not recommended for metagenomes.

Expand Down Expand Up @@ -31,3 +31,22 @@ plassembler run -d Plassembler_DB -l ERR7287988.fastq.gz -1 ERR7255689_1.fastq.g
`plassembler` took around 8 hours (wall clock) to finish and excitingly we assembled all 7 bacterial chromosomes using Flye (unsurprising!) along with the 5 plasmids indicated in the ground truth (1 _E. coli_ 100kbp, 1 _S. enterica_ 49kbp and 3 small _S. aureus_ plasmids (6, 2 and 2 kbp)) with genome fraction 100% from QUAST.

So in theory `plassembler` might work on metagenomes, but I would caution against using it, for now.


Contigs 34, 61, 87, 101 and 109 match what was found in the ground truth.

| contig | length | mean_depth_short | circularity | PLSDB_hit | ACC_NUCCORE | Description_NUCCORE | plasmid_copy_number_short | plasmid_copy_number_long |
| ------ | ------ | ---------------- | ------------ | --------- | ------------- | ------------------------------------------------------------------------------------------------------------------- | ------------------------- | ------------------------ |
| 34 | 110007 | 336.5 | circular | Yes | NZ_CP061531.1 | Escherichia coli strain WEM25 plasmid p1, complete sequence | 1.67 | 1.37 |
| 61 | 49661 | 357.16 | not_circular | Yes | NZ_CP012345.2 | Salmonella enterica subsp. enterica serovar Choleraesuis str. ATCC 10708 plasmid pCFSAN000679_01, complete sequence | 1.78 | 3.17 |
| 83 | 9628 | 39.11 | not_circular | Yes | NZ_CP069918.1 | Klebsiella oxytoca strain FDAARGOS_1334 plasmid unnamed7 | 0.19 | 0 |
| 87 | 6367 | 9554.23 | circular | Yes | NZ_CP013628.1 | Staphylococcus aureus strain RIVM4293 plasmid pRIVM4293, complete sequence. | 47.54 | 12.67 |
| 91 | 5355 | 14.61 | not_circular | Yes | NZ_CP068597.1 | Paenibacillus sonchi strain LMG 24727 plasmid unnamed2, complete sequence | 0.07 | 0 |
| 93 | 5010 | 13.32 | not_circular | Yes | NZ_CP068597.1 | Paenibacillus sonchi strain LMG 24727 plasmid unnamed2, complete sequence | 0.07 | 0 |
| 101 | 2993 | 2561.92 | circular | Yes | NZ_MH785226.1 | Staphylococcus aureus strain ph1 plasmid pRIVM1295-2, complete sequence | 12.75 | 1.65 |
| 103 | 2789 | 1018.1 | not_circular | Yes | CP048737.1 | Enterobacter sp. T2 plasmid unnamed1, complete sequence | 5.07 | 4.75 |
| 106 | 2667 | 1045.66 | not_circular | Yes | NZ_CP066061.1 | Actinomyces oris strain FDAARGOS_1051 plasmid unnamed | 5.2 | 4.79 |
| 108 | 2337 | 16.17 | not_circular | Yes | NZ_CP069918.1 | Klebsiella oxytoca strain FDAARGOS_1334 plasmid unnamed7 | 0.08 | 0 |
| 109 | 2216 | 2188.82 | circular | Yes | NZ_CP013624.1 | Staphylococcus aureus strain RIVM1076 plasmid pRIVM1076, complete sequence. | 10.89 | 1.08 |
| 141 | 1049 | 1015.41 | not_circular | Yes | NZ_CP066061.1 | Actinomyces oris strain FDAARGOS_1051 plasmid unnamed | 5.05 | 4.77 |
| 145 | 830 | 930.78 | not_circular | Yes | NZ_CP066061.1 | Actinomyces oris strain FDAARGOS_1051 plasmid unnamed |

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