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