QUASR
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing
Building the QUASR app
1. Open a command line terminal
2. Clone the git project
3. cd into the project folder
4. run: ant
5. A folder (quasr_dist) one level up from the project folder will be created.
6. cd into it and run: java -jar readsetProcessor.jar
USAGE
-h/--help Print this usage information
-v/--version Print version number
* -i/--infile SE or single-PE FASTQ (or GZIPed FASTQ) or SFF
-r/--reverse FASTQ (or GZIPed FASTQ) or SFF containing reverse mates
-2/--paired Input file is paired-end. Only necessary if 1 file parsed
* -o/--outprefix Output directory and file prefix
-z/--gzip Compress output files to GZIPed FASTQ
-n/--num Number of records to parse at a time [default: 100]
-I/--illumina Quality scores encoded with Illumina offset (+64) instead of Sanger (+33)
Demultiplex:
-M/--mids Comma-separated MIDs to be parsed. Accepts ranges
+ -s/--sequence Demultiplex by parsing sequence. Mutually-exlusive with -d
-c/--custom File containing custom MID sequences. Only allowed with -s
-O/--offset Maximum offset MID can be within a read. Only allowed with -s [default: 10]
+ -H/--header Demultiplex by parsing header. Mutually exclusive with -s
-P/--pattern Regex to match in header. Only allowed with -d [default: "#(\d+)/\d$"]
Duplicate removal:
-d/--duplicate Perform duplicate removal
Primer removal:
-p/--primer File containing primer sequences
-L/--leeway Maximum distance primer can be within a read [default: 40]
Quality control:
-q/--quality Perform quality control
-l/--length Minimum read length cutoff [default: 50]
-m/--median Median read quality cutoff [default: 20.0]
QA graphing:
-g/--graph Perform quality assurance graphing
-R/--Rpath Path to R binary (only needs to be set once if current stored path doesn't work)
-w/--window Window length for 3'-cross sectional dropoff [default:50]
[NOTE]: Options marked * are mandatory. Those marked + are mandatory but mutually-exclusive All others are optional. All steps are optional. Steps are performed in the order shown.