determine-phred
command-line tools for processing biological sequencing data
Install
- All systems
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curl cmd.cat/determine-phred.sh
- Debian
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apt-get install ea-utils - Ubuntu
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apt-get install ea-utils - Kali Linux
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apt-get install ea-utils - Windows (WSL2)
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sudo apt-get updatesudo apt-get install ea-utils - Raspbian
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apt-get install ea-utils - Dockerfile
- dockerfile.run/determine-phred
ea-utils
command-line tools for processing biological sequencing data
Ea-utils provides a set of 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. Main Tools are: * 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.