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updated readme
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farchaab committed Oct 4, 2023
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Expand Up @@ -73,14 +73,14 @@ Compressed fasta files are saved in the assemblies directory with assembly, sequ

#### Assembly summary

| entry | database | db_uid | asm_name | organism | asm_release_date | asm_status | refseq_category | contig_count | contig_n50 | genome_size | coverage | asm_method | seq_tech | path |
| :------ | :------- | :------- | :----------- | :------------------------------------------------------------------ | :--------------- | :-------------- | :-------------------- | :----------- | :--------- | :---------- | :------- | :------------------------- | :--------------------------------------------------- | :----------------------------------------------------------------------- |
| 1290 | refseq | 7934998 | ASM381250v1 | Staphylococcus hominis (firmicutes) | 2018/11/26 00:00 | Complete Genome | representative genome | 3 | 2220494 | 2257431 | 19.64 | SMRT v. 2.3.0, HGAP v. 3.0 | PacBio; Illumina | /absolute/path/to/assemblies/GCF_003812505.1_ASM381250v1_genomic.fna.gz |
| 1290 | refseq | 15589428 | ASM973011v1 | Staphylococcus hominis (firmicutes) | 2019/12/09 00:00 | Complete Genome | na | 4 | 2178824 | 2242116 | 1980.61 | canu v. 1.4 | Pacbio; Illumina | /absolute/path/to/assemblies/GCF_009730115.1_ASM973011v1_genomic.fna.gz |
| 1290 | refseq | 15589668 | ASM973013v1 | Staphylococcus hominis (firmicutes) | 2019/12/09 00:00 | Complete Genome | na | 3 | 2323613 | 2372192 | 1875.96 | SMRT v. 2.3.0, HGAP v. 3 | Pacbio; Illumina | /absolute/path/to/assemblies/GCF_009730135.1_ASM973013v1_genomic.fna.gz |
| 1813735 | refseq | 6612678 | ASM161886v1 | Luteitalea pratensis (bacteria) | 2018/06/07 00:00 | Complete Genome | representative genome | 1 | 7480314 | 7480314 | 112.0 | HGAP SMRTPortal v. 2.3.0 | PacBio; Illumina HiSeq 2500 | /absolute/path/to/assemblies/GCF_001618865.1_ASM161886v1_genomic.fna.gz |
| 1813735 | refseq | 31969758 | ASM1686548v2 | Luteitalea sp. TBR-22 (bacteria) | 2022/02/22 00:00 | Complete Genome | na | 1 | 6468984 | 6468984 | 54.0 | HybridSPAdes v. 3.13.0 | Illumina Miseq system; Oxford Nanopore MinION system | /absolute/path/to/assemblies/GCF_016865485.1_ASM1686548v2_genomic.fna.gz |
| 114185 | refseq | 421728 | ASM28727v1 | Candidatus Carsonella ruddii HC isolate Thao2000 (g-proteobacteria) | 2012/09/07 00:00 | Complete Genome | representative genome | 1 | 166163 | 166163 | | | | /absolute/path/to/assemblies/GCF_000287275.1_ASM28727v1_genomic.fna.gz |
| entry | database | db_uid | asm_name | organism | asm_release_date | asm_status | refseq_category | contig_count | contig_n50 | genome_size | coverage | asm_method | seq_tech | path |
| :------ | :------- | :------- | :----------- | :------------------------------------------------------------------ | :--------------- | :-------------- | :-------------------- | :----------- | :--------- | :---------- | :------- | :------------------------- | :--------------------------------------------------- | :----------------------------------------------------------------------------------------------- |
| 1290 | refseq | 7934998 | ASM381250v1 | Staphylococcus hominis (firmicutes) | 2018/11/26 00:00 | Complete Genome | representative genome | 3 | 2220494 | 2257431 | 19.64 | SMRT v. 2.3.0, HGAP v. 3.0 | PacBio; Illumina | /home/fchaaban/tests/assembly_finder/test/assemblies/GCF_003812505.1_ASM381250v1_genomic.fna.gz |
| 1290 | refseq | 15589428 | ASM973011v1 | Staphylococcus hominis (firmicutes) | 2019/12/09 00:00 | Complete Genome | na | 4 | 2178824 | 2242116 | 1980.61 | canu v. 1.4 | Pacbio; Illumina | /home/fchaaban/tests/assembly_finder/test/assemblies/GCF_009730115.1_ASM973011v1_genomic.fna.gz |
| 1290 | refseq | 15589668 | ASM973013v1 | Staphylococcus hominis (firmicutes) | 2019/12/09 00:00 | Complete Genome | na | 3 | 2323613 | 2372192 | 1875.96 | SMRT v. 2.3.0, HGAP v. 3 | Pacbio; Illumina | /home/fchaaban/tests/assembly_finder/test/assemblies/GCF_009730135.1_ASM973013v1_genomic.fna.gz |
| 114185 | refseq | 421728 | ASM28727v1 | Candidatus Carsonella ruddii HC isolate Thao2000 (g-proteobacteria) | 2012/09/07 00:00 | Complete Genome | representative genome | 1 | 166163 | 166163 | | | | /home/fchaaban/tests/assembly_finder/test/assemblies/GCF_000287275.1_ASM28727v1_genomic.fna.gz |
| 1813735 | refseq | 6612678 | ASM161886v1 | Luteitalea pratensis (bacteria) | 2018/06/07 00:00 | Complete Genome | representative genome | 1 | 7480314 | 7480314 | 112.0 | HGAP SMRTPortal v. 2.3.0 | PacBio; Illumina HiSeq 2500 | /home/fchaaban/tests/assembly_finder/test/assemblies/GCF_001618865.1_ASM161886v1_genomic.fna.gz |
| 1813735 | refseq | 31969758 | ASM1686548v2 | Luteitalea sp. TBR-22 (bacteria) | 2022/02/22 00:00 | Complete Genome | na | 1 | 6468984 | 6468984 | 54.0 | HybridSPAdes v. 3.13.0 | Illumina Miseq system; Oxford Nanopore MinION system | /home/fchaaban/tests/assembly_finder/test/assemblies/GCF_016865485.1_ASM1686548v2_genomic.fna.gz |

#### Taxonomy summary

Expand All @@ -89,17 +89,14 @@ Compressed fasta files are saved in the assemblies directory with assembly, sequ
| ASM381250v1 | Staphylococcus hominis (firmicutes) | strain | FDAARGOS_575 | 1290 | Bacteria | Bacillota | Bacilli | Bacillales | Staphylococcaceae | Staphylococcus | Staphylococcus hominis |
| ASM973011v1 | Staphylococcus hominis (firmicutes) | strain | FDAARGOS_747 | 1290 | Bacteria | Bacillota | Bacilli | Bacillales | Staphylococcaceae | Staphylococcus | Staphylococcus hominis |
| ASM973013v1 | Staphylococcus hominis (firmicutes) | strain | FDAARGOS_746 | 1290 | Bacteria | Bacillota | Bacilli | Bacillales | Staphylococcaceae | Staphylococcus | Staphylococcus hominis |
| ASM28727v1 | Candidatus Carsonella ruddii HC isolate Thao2000 (g-proteobacteria) | strain | HC | 1202538 | Bacteria | Pseudomonadota | Gammaproteobacteria | Oceanospirillales | Halomonadaceae | Candidatus Carsonella | Candidatus Carsonella ruddii |
| ASM161886v1 | Luteitalea pratensis (bacteria) | strain | DSM 100886 | 1855912 | Bacteria | Acidobacteriota | Vicinamibacteria | Vicinamibacterales | Vicinamibacteraceae | Luteitalea | Luteitalea pratensis |
| ASM1686548v2 | Luteitalea sp. TBR-22 (bacteria) | strain | TBR-22 | 2802971 | Bacteria | Acidobacteriota | Vicinamibacteria | Vicinamibacterales | Vicinamibacteraceae | Luteitalea | Luteitalea sp. TBR-22 |
| ASM28727v1 | Candidatus Carsonella ruddii HC isolate Thao2000 (g-proteobacteria) | strain | HC | 1202538 | Bacteria | Pseudomonadota | Gammaproteobacteria | Oceanospirillales | Halomonadaceae | Candidatus Carsonella | Candidatus Carsonella ruddii |

#### Sequence summary

| asm_name | organism | taxid | genbank_accn | refseq_accn | assigned_molecule_location/type | sequence_length |
| :----------- | :------------------------------------------------------------------ | :------ | :----------- | :------------ | :------------------------------ | :-------------- |
| ASM161886v1 | Luteitalea pratensis (bacteria) | 1855912 | CP015136.1 | NZ_CP015136.1 | Chromosome | 7480314 |
| ASM1686548v2 | Luteitalea sp. TBR-22 (bacteria) | 2802971 | AP024452.2 | NZ_AP024452.1 | Chromosome | 6468984 |
| ASM28727v1 | Candidatus Carsonella ruddii HC isolate Thao2000 (g-proteobacteria) | 1202538 | CP003543.1 | NC_018416.1 | Chromosome | 166163 |
| ASM381250v1 | Staphylococcus hominis (firmicutes) | 1290 | CP033732.1 | NZ_CP033732.1 | Chromosome | 2220494 |
| ASM381250v1 | Staphylococcus hominis (firmicutes) | 1290 | CP033731.1 | NZ_CP033731.1 | Plasmid | 32498 |
| ASM381250v1 | Staphylococcus hominis (firmicutes) | 1290 | CP033733.1 | NZ_CP033733.1 | Plasmid | 4439 |
Expand All @@ -110,6 +107,9 @@ Compressed fasta files are saved in the assemblies directory with assembly, sequ
| ASM973013v1 | Staphylococcus hominis (firmicutes) | 1290 | CP046306.1 | NZ_CP046306.1 | Chromosome | 2323613 |
| ASM973013v1 | Staphylococcus hominis (firmicutes) | 1290 | CP046304.1 | NZ_CP046304.1 | Plasmid | 23366 |
| ASM973013v1 | Staphylococcus hominis (firmicutes) | 1290 | CP046305.1 | NZ_CP046305.1 | Plasmid | 25213 |
| ASM28727v1 | Candidatus Carsonella ruddii HC isolate Thao2000 (g-proteobacteria) | 1202538 | CP003543.1 | NC_018416.1 | Chromosome | 166163 |
| ASM161886v1 | Luteitalea pratensis (bacteria) | 1855912 | CP015136.1 | NZ_CP015136.1 | Chromosome | 7480314 |
| ASM1686548v2 | Luteitalea sp. TBR-22 (bacteria) | 2802971 | AP024452.2 | NZ_AP024452.1 | Chromosome | 6468984 |

## Examples

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