Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline, but should work with any FASTQs.
- fastq-mcf - Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering.
- fastq-multx - Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not.
- fastq-join - Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same "squared distance for anchored alignment" as other tools.
- varcall - Takes a pileup and calculates variants in a more easily parameterized manner than some other tools.
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