README file for data release @ http://andersen-lab.com/travel-related-cases-florida/

README.md

Data

All the files can be accessed here: https://www.dropbox.com/sh/h2rt76o42qqnltx/AADOJveBz9p5D76nKPvMI9i6a?dl=0

Protocol can be found here: https://docs.google.com/document/d/1PilT4w5jHO-ROsE8TL5WBGa0wSCdTHAsNl1LIOYiTgk/

Methods

• Human reads removed using bmtagger and Kraken.
• Adapters trimmed using 'palindrome' mode in Trimmomatic.
• Alignment done using Novoalign.
• QC reports generated using FastQC.
• Metagenomic analysis done using Kraken and visualized using Krona Tools.
• Bam file operations were SAMtools, Picard.
• Depth and coverage calculations were done using SAMtools and bedtools

Samples

Key

|-----+------------|
| Abb | Type       |
|-----+------------|
| RN  | RNA        |
| SA  | Saliva     |
| UR  | Urine      |
| SS  | Seed Stock |
|-----+------------|

Naming Scheme

ZF10.c1.UR.a1.l1.r1.S4.L001.R1
<StudyName><Sample Number>.<Collection Number>.<Sample Type>.<Aliquot Number>.<Library Number>.<Run Number>

GN2.c1.RN.a1.l1.r1.S1.L001 is the water control. ZP1.c1.SS.a1.l1.r1, ZP1.c1.SS.a2.l2.r1 and ZP1.c1.SS.a3.l3.r1 are positive controls. The positive control is the PRVABC59 strain of Zika virus.

Percentage Coverage and Average Depth

|-----------------------------+---------------------+----------------|
| Sample                      | Percentage Coverage | Average  Depth |
|-----------------------------+---------------------+----------------|
| ZF1.c1.Sa.a1.l1.r1.S2.L001  |   98.36404663407295 |  60763.4654005 |
| ZF10.c1.UR.a1.l1.r1.S4.L001 |   98.37344866491162 |  78627.7615645 |
| ZF18.c1.UR.a1.l1.r1.S5.L001 |   97.27341105678826 |  48582.6466717 |
| ZF8.c1.UR.a1.l1.r1.S3.L001  |   98.35464460323429 |  47751.4419895 |
| ZP1.c1.SS.a1.l1.r1.S6.L001  |               100.0 |  69933.1217563 |
| ZP1.c1.SS.a2.l2.r1.S7.L001  |   99.74614516735615 |  83580.8614141 |
| ZP1.c1.SS.a3.l3.r1.S8.L001  |   99.64272282813089 |  53952.3396954 |
|-----------------------------+---------------------+----------------|

Files

Description of folders

• bams_raw

The bam files after depleting human reads.

• bams_trimmed

The raw bam files trimmed to remove adapter sequences.

• bams_aligned

The trimmed bam files aligned to the reference zika virus sequence(GenBank: KU853012.1).

• fastqc

The quality reports for the raw bam files and the trimmed bam files.

• kraken_metagenomic_analyses

The kraken outputs visualized using krona tools.

File structure

.
|-- analyses
|   |-- coverages.pdf
|   |-- root-to-tip.jpg
|   |-- tree_rooted_raxml.nex
|   |-- tree_rooted_raxml.nex.jpg
|   `-- tree_rooted_raxml.nex.pdf
|-- bams_aligned
|   |-- ZF1.c1.Sa.a1.l1.r1.S2.L001.aligned.1471381587.bam
|   |-- ZF10.c1.UR.a1.l1.r1.S4.L001.aligned.1471381587.bam
|   |-- ZF18.c1.UR.a1.l1.r1.S5.L001.aligned.1471381587.bam
|   |-- ZF8.c1.UR.a1.l1.r1.S3.L001.aligned.1471381587.bam
|   |-- ZP1.c1.SS.a1.l1.r1.S6.L001.aligned.1471381587.bam
|   |-- ZP1.c1.SS.a2.l2.r1.S7.L001.aligned.1471381587.bam
|   `-- ZP1.c1.SS.a3.l3.r1.S8.L001.aligned.1471381587.bam
|-- bams_raw
|   |-- GN2.c1.RN.a1.l1.r1.S1.L001.1471381587.bam
|   |-- ZF1.c1.Sa.a1.l1.r1.S2.L001.1471381587.bam
|   |-- ZF10.c1.UR.a1.l1.r1.S4.L001.1471381587.bam
|   |-- ZF18.c1.UR.a1.l1.r1.S5.L001.1471381587.bam
|   |-- ZF8.c1.UR.a1.l1.r1.S3.L001.1471381587.bam
|   |-- ZP1.c1.SS.a1.l1.r1.S6.L001.1471381587.bam
|   |-- ZP1.c1.SS.a2.l2.r1.S7.L001.1471381587.bam
|   `-- ZP1.c1.SS.a3.l3.r1.S8.L001.1471381587.bam
|-- bams_trimmed
|   |-- GN2.c1.RN.a1.l1.r1.S1.L001.trimmed.1471381587.bam
|   |-- ZF1.c1.Sa.a1.l1.r1.S2.L001.trimmed.1471381587.bam
|   |-- ZF10.c1.UR.a1.l1.r1.S4.L001.trimmed.1471381587.bam
|   |-- ZF18.c1.UR.a1.l1.r1.S5.L001.trimmed.1471381587.bam
|   |-- ZF8.c1.UR.a1.l1.r1.S3.L001.trimmed.1471381587.bam
|   |-- ZP1.c1.SS.a1.l1.r1.S6.L001.trimmed.1471381587.bam
|   |-- ZP1.c1.SS.a2.l2.r1.S7.L001.trimmed.1471381587.bam
|   `-- ZP1.c1.SS.a3.l3.r1.S8.L001.trimmed.1471381587.bam
|-- consensus_sequences
|   |-- Florida_ex-Cuba_2016_06_02_ZF10.c1.UR.a1.l1.r1.fasta
|   |-- Florida_ex-Martinigue_2016_03_07_ZF1.c1.Sa.a1.l1.r1.fasta
|   |-- Florida_ex-Puerto_Rico_2016_06_13_ZF8.c1.UR.a1.l1.r1.fasta
|   |-- Positive\ control\ -\ ZP1.c1.SS.a1.l1.r1.fasta
|   `-- Reference\ Zika\ virus\ -\ KU853012.fasta
|-- fastqc
|   |-- GN2.c1.RN.a1.l1.r1.S1.L001.1471381587.fastqc.zip
|   |-- GN2.c1.RN.a1.l1.r1.S1.L001.trimmed.1471381587.fastqc.zip
|   |-- ZF1.c1.Sa.a1.l1.r1.S2.L001.1471381587.fastqc.zip
|   |-- ZF1.c1.Sa.a1.l1.r1.S2.L001.trimmed.1471381587.fastqc.zip
|   |-- ZF10.c1.UR.a1.l1.r1.S4.L001.1471381587.fastqc.zip
|   |-- ZF10.c1.UR.a1.l1.r1.S4.L001.trimmed.1471381587.fastqc.zip
|   |-- ZF18.c1.UR.a1.l1.r1.S5.L001.1471381587.fastqc.zip
|   |-- ZF18.c1.UR.a1.l1.r1.S5.L001.trimmed.1471381587.fastqc.zip
|   |-- ZF8.c1.UR.a1.l1.r1.S3.L001.1471381587.fastqc.zip
|   |-- ZF8.c1.UR.a1.l1.r1.S3.L001.trimmed.1471381587.fastqc.zip
|   |-- ZP1.c1.SS.a1.l1.r1.S6.L001.1471381587.fastqc.zip
|   |-- ZP1.c1.SS.a1.l1.r1.S6.L001.trimmed.1471381587.fastqc.zip
|   |-- ZP1.c1.SS.a2.l2.r1.S7.L001.1471381587.fastqc.zip
|   |-- ZP1.c1.SS.a2.l2.r1.S7.L001.trimmed.1471381587.fastqc.zip
|   |-- ZP1.c1.SS.a3.l3.r1.S8.L001.1471381587.fastqc.zip
|   `-- ZP1.c1.SS.a3.l3.r1.S8.L001.trimmed.1471381587.fastqc.zip
`-- kraken_metagenomic_analyses
    |-- ZF1.c1.Sa.a1.l1.r1.S2.L001.1.1471381587.zip
    |-- ZF1.c1.Sa.a1.l1.r1.S2.L001.1.trimmed.1471381587.zip
    |-- ZF10.c1.UR.a1.l1.r1.S4.L001.1.1471381587.zip
    |-- ZF10.c1.UR.a1.l1.r1.S4.L001.1.trimmed.1471381587.zip
    |-- ZF18.c1.UR.a1.l1.r1.S5.L001.1.1471381587.zip
    |-- ZF18.c1.UR.a1.l1.r1.S5.L001.1.trimmed.1471381587.zip
    |-- ZF8.c1.UR.a1.l1.r1.S3.L001.1.1471381587.zip
    |-- ZF8.c1.UR.a1.l1.r1.S3.L001.1.trimmed.1471381587.zip
    |-- ZP1.c1.SS.a1.l1.r1.S6.L001.1471381587.zip
    |-- ZP1.c1.SS.a1.l1.r1.S6.L001.trimmed.1471381587.zip
    |-- ZP1.c1.SS.a2.l2.r1.S7.L001.1471381587.zip
    |-- ZP1.c1.SS.a2.l2.r1.S7.L001.trimmed.1471381587.zip
    |-- ZP1.c1.SS.a3.l3.r1.S8.L001.1471381587.zip
    `-- ZP1.c1.SS.a3.l3.r1.S8.L001.trimmed.1471381587.zip