资 源 简 介
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.
Overview:
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
