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Output trusted regions from raw sequencing data.
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syrah reads sequences from stdin and outputs subsequences containing solid or trusted k-mers suitable for counting or MinHashing.

syrah automatically exits when it has seen enough solid k-mers.


You can specify the number of solid k-mers with -n.

You can set the k-mer size with -k.

You can eliminate all output with -q.

There are no other options because options lead to anger. Anger leads to hate. Hate leads to suffering.

Use cases

The primary use case for the moment is to extract a subset of solid k-mers for loading into sourmash signatures. For example,

dump-fastq -A $SRA_ID -Z | syrah | sourmash compute - -o out.sig

will extract the first 1m solid k-mers from the given SRA data set and feed them into sourmash to compute a signature. Once enough k-mers are found, syrah will terminate the stream.

The default parameters are designed for small microbial genomes (where 1m k-mers is usually between 20-50% of the genome) and may be OK for metagenome and transcriptome overlap analysis, but for other situations you may need to vary -n.

CTB 12/2016

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