Cubic Genomics Project Information
| Project ID |
Probiotics_Kraken231229112612_0 |
| Sample Name | CH3456_S3_L001 |
| Sequence Type | Paired-End |
| Execute date | 2023 12/29 11:27:41 |
| P.I. | Dr.Chen AH |
| ProjectPath | /project/Probiotics_Kraken231229112612_0/ |
| Backup Path | /backup/ |
| Classifier | db_k2all |
| |
|
Result
｜ Probiotics panel result
| Sample | CH3456_S3_L001 |
|---|---|
| Bifidobacterium | ND |
| Lactobacillus | ND |
| Lactobacillus acidophilus | 0.00%(1) |
| Lactobacillus casei | ND |
｜ Taxonomy result
| Total Sequences Processed |
93431 |
| Sequences Classified |
93418 |
| Sequences Unclassified |
13 |
| Class | Percentage(count) |
| Total | 93418.0 |
| Prevotella copri | 39.24%(36658) |
| Eubacterium ventriosum | 10.76%(10054) |
| Phascolarctobacterium faecium | 5.63%(5262) |
| Faecalibacterium prausnitzii | 4.63%(4328) |
| Phocaeicola salanitronis | 2.90%(2705) |
| Phocaeicola coprophilus | 1.83%(1705) |
| Alistipes senegalensis | 1.74%(1624) |
| Parabacteroides johnsonii | 1.69%(1578) |
| Lachnospira eligens | 1.13%(1052) |
| Haemophilus parainfluenzae | 1.01%(939) |
Total Species-level Taxonomic Categories Identified:366.
This table shows the top of classifications.
Note: The "Other" category in this pie chart is the sum of all classifications with less than 1 % abundance.
| Class | Percentage(count) |
| Total | 93418.0 |
| Prevotella | 41.09%(38390) |
| Eubacterium | 10.77%(10060) |
| Faecalibacterium | 6.42%(5993) |
| Phascolarctobacterium | 5.64%(5270) |
| Phocaeicola | 5.40%(5046) |
| Clostridium | 4.43%(4142) |
| Parabacteroides | 3.17%(2965) |
| Alistipes | 1.93%(1807) |
| Turicibacter | 1.76%(1641) |
| Haemophilus | 1.36%(1273) |
Total Genus-level Taxonomic Categories Identified:240.
This table shows the top of classifications.
Note: The "Other" category in this pie chart is the sum of all classifications with less than 1 % abundance.
Supplement
Pipeline Information
Fastp : v0.23.2 https://github.com/OpenGene/fastp
BWA: v0.7.17 https://github.com/lh3/bwa
Samtools: v1.15 https://github.com/samtools/
Unicycler : v０.5.0 https://github.com/rrwick/Unicycler
Kraken2 : v2.1.2 https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown
Reference : Sus_scrofa.Sscrofa11.1
Database Information
Source: https://benlangmead.github.io/aws-indexes/k2
db_k2all: PlusPFP-16
db_SILVA132: SILVA 132
db_SILVA138: SILVA 138
db_RDP: RDP 11.5
db_Greengenes: Greengenes 13.5
Samples Information
| SampleName | R1 | R2 |
| CH3456_S3_L001 | raw/CH3456_S3_L001_R1.fastq.gz | raw/CH3456_S3_L001_R2.fastq.gz |
