Bioinformática

Ofrecemos servicios y asesoría de análisis bioinformáticos para los siguientes análisis, varios de éstos análisis están integrados a la secuenciación que ofrecemos.

  • Ensamble y anotación de genomas microbianos
  • Comparación de genomas bacterianos (core y pangenome)
  • Filogenia genómica
  • Diversidad metagenómica 16S/18S
  • Metagenómica shotgun (taxonómica y funcional)

Ejemplos de resultados 16S

Va desde la limpieza de secuencias, ensamble de secuencias pareadas, eliminación de secuencias quiméricas y clasificación de OTUs con bases de datos curadas. Usamos unos scripts propios disponibles libremente en Github como metagenomic_pipeline.

Este análisis incluye los siguientes archivos:

- Main table with OTUs found per sample: otus.tsv
- Log of the bioinformatic processes done: mg_classifier.log
OTU_tables subidrectory
   - Excel-type table with OTUs order from most abundant: otus.xls
   - Table with the number of sequences per taxon: OTUs_summary.tsv
   - Table with genera found per sample: genus.tsv
   - Table with families found per sample: family.tsv
   - Table with phyla found per sample: phylum.tsv
   - File with the samples first and the taxonomy, useful to make KRONA charts: samples-tax.tsv
   - Files with core taxa: core_phylum.txt and core_family.txt
   STAMP subidrectory
     - Table of results to be analyzed with STAMP
       Linux file: bacteria.spf
       Windows file: bacteria.win.spf
   QIIME subidrectory
     - OTU table useful for qiime, ampvis2, etc.: OTU_table.tsv and otus.txt
   Phyloseq subidrectory
     - Taxonomy table: taxonomy_table.tsv
     - Table of OTUs: otus_table.tsv
Diversity subdirectory
   - Alpha diversity indexes: alpha.txt
   - Selected alpha diversity indexes: alpha_indexes.tsv
   - Beta diversity indexes: beta matrix (.txt) and trees (.tree)
   - Rarefaction analyses of samples: rare.txt
Plot subdirectory
   - File for plotting the 15 most abundant families: families-plot.csv
   - File for plotting all the phyla: phyla_plot.csv
   - File for plotting only the 15 most abundant phyla: phyla15_plot.csv

Reporte

Generamos un reporte para cada paso del análisis bioinformático, a continuación se muestra un ejemplo de cada uno de los reportes:

pair-end_cleaner v0.9.9
Laboratorio de Genomica Microbiana, CIAD AC.
https://github.com/GenomicaMicrob/pair-end_cleaner
Date: 11-05-2018 10:09

This script eliminated with Cutadapt low quality bases (< Q20), N's, and removed
short pair-end sequences (< 149 bases). After this clean-up, it assembled with
PEAR both pair-end sequences into one with a minimum assembly length of 240 
bases and a maximum length of 300 bases for the \e[1m16S_V4\e[0m region.

Total runtime: 0 hrs 1 min and 23 sec

RESULTS

Number of samples processed:         19
Total number of fastq sequences:     144,567
Total number of assembled sequences: 143,143
chimera_detector version v1.3.5
Laboratorio de Genomica Microbiana, CIAD AC.
https://github.com/GenomicaMicrob
Date: 2018-05-11_10:11

This script searched for chimeras in the files provided by comparing
the sequences with the SILVA_v128 database with vsearch.
If a query sequence had a match (by 97% similarity) in the database,
it was not considered a chimera.

RESULTS
A total of 19 files were analysed.

sample  chimera-free chimera
F3D141 5,363 546
F3D142 2,824 321
F3D143 2,788 366
F3D144 4,236 524
F3D145 6,541 740
F3D146 4,406 564
F3D147 14,797 2,074
F3D148 10,977 1,321
F3D149 11,640 1,327
F3D150 4,829 635
F3D1 5,348 453
F3D2 17,933 1,514
F3D3 6,032 676
F3D5 4,065 336
F3D6 7,346 556
F3D7 4,680 398
F3D8 4,951 299
F3D9 6,549 463
Mock 4,621 104
_______________________________________________________________________________
Metagenomic Sequence Classifier v1.8.0
Laboratorio de Genomica Microbiana, CIAD AC.
https://github.com/GenomicaMicrob/mg_classifier
Date: 20-09-2019 11:25

129,926 sequences were classified from 19 files with the EzBioCloud-LGM v311218 database.
Database remarks: Curated database in UDB format, it is a merge between the v1.5 and new taxa up to the 31 Dec 2018, dereplicated.
Sequences were clustered at 0.97% similarity, and singletons were removed.
The following thresholds were used to delimit taxa: species 97, genus 94, family 86.5, order 82, class 78.5, and phylum 75. (based on Yarza et al. 2014. Nat Rev Microbiol 12:635-645 http://www.nature.com/nrmicro/journal/v12/n9/full/nrmicro3330.html).

Total runtime: 0 hrs 0 min and 27 sec done with 2 CPUs out of 64 available
and processing 4 samples simultaneously.

---SUMMARY OF RESULTS---

Total OTUs assigned to Archaea 0, Bacteria 321, and to Eukarya 5.
Total number of different bacterial phyla found: 7
Total number of different bacterial families found: 32
Total number of different bacterial genera found: 118
Number of families found in all samples (core families): 3