- Python 3 (tested on Python 3.6.3). Required python packages:
- cutadapt (tested on 1.16)
- numpy (tested on 1.14.1)
- biopython (tested on 1.70)
- pandas (tested on 0.22.0)
- BWA (Burrows-Wheeler Aligner). Tested on 0.7.17-r1188. Download here
- ea-utils/fastq-join. Tested on 1.04.807. Download here
- fastq_quality_filter from fastx-toolkit. Tested on 0.0.13. Download here
This tool was was designed to run from a linux terminal. Tested on Ubuntu 17.10 (x86-64 architecture).
$./genotyping_pipeline.sh \
FASTQDIR \
ADAPTERS_FILE \
REFERENCE \
RESULTS_DIR
FASTQDIR
Folder where all the fastq files are contained. Only Illumina pair-end sequencing from PCR amplicons is accepted. One sample pair per file.
IMPORTANT: *.fastq or *.fastq.gz are accepted. Read 1 must be specified
as R1 and read 2 as R2 in the filename. Sample name will be taken
from the string before the first _ character that should be present in
the filename.
Examples of valid fastq filenames:
2_S1_L001_R1_001.fastq.gz # sample name = "2"; read = 1.
sample1_R2.fastq # sample name = "sample1", read = 2.
ADAPTERS_FILE
Path to a fasta file containing adapter sequences used to
create amplicons for sequencing. Only two adapters allowed, named as
>Forward and >Reverse (>F and >R or >f and >r is sufficient).
Adapter sequence has to span only one line.
REFERENCE
Path to a fasta file containing HCV reference sequences. Sequence names should follow the convention TS_XXXXX, where T is HCV type, S is HCV subtype and XXXXX is the sequence identifier. HCV reference genomes are included in HCV_references/HCV_genotypes.fasta with date January 1st 2017, downloaded from here
RESULTS_DIR
Path to a folder where output results. If WORKINGDIR does not exist it will be created. If WORKINGDIR exists, program exits with ERROR message.
Results will be written to RESULTS_DIR folder (summary table at RESULTS_DIR/results.csv).
IMPORTANT!: arguments order should be kept.