From e8e2e26afffee868d963bf221e2de970a911c488 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Fri, 2 Jun 2023 15:03:25 +0930 Subject: [PATCH] metagenome2 --- docs/metagenomics.md | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/docs/metagenomics.md b/docs/metagenomics.md index b69b7e0..7bd55e7 100644 --- a/docs/metagenomics.md +++ b/docs/metagenomics.md @@ -1,4 +1,4 @@ -##### 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. @@ -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 | \ No newline at end of file