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some proofing
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lskatz committed Feb 5, 2024
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Expand Up @@ -46,13 +46,13 @@ Continuous integration was implemented in GitHub Actions for unit testing.
Each executable is tested to make sure the expected output is obtained with each `git push` event.
We also used GitHub Actions to automatically create a Docker container which is also available on the GitHub repo.

![Benchmarks comparing fasten with other analogous tools. From left to right, then to bottom: Trimming with a minimum quality score; converting fastq to fasta; interleaving R1 and R2 reads; kmer counting; normalizing read depth using kmer coverage; Searching for a sequence in a fastq file; downsampling reads; sorting fastq entries by either sequence or ID; and converting nonstandard fastq files to a format whose entries are four lines each, and selecting the first 100.\label{fig:benchmarks}](benchmarks.png)
![Benchmarks comparing fasten with other analogous tools. From left to right, then to bottom: Trimming with a minimum quality score; converting fastq to fasta; interleaving R1 and R2 reads; kmer counting; normalizing read depth using kmer coverage; searching for a sequence in a fastq file; downsampling reads; sorting fastq entries by either sequence or ID; and converting nonstandard fastq files to a format whose entries are four lines each, and selecting the first 100.\label{fig:benchmarks}](benchmarks.png)

## Conclusions

Fasten is a powerful manipulation suite for interleaved fastq files, written in Rust.
We benchmarked Fasten on several categories.
It has strengths as shown in Figure 1 but it does not occupy the fastest position in all cases.
It exhibits strengths as shown in Figure 1 but it does not consistently hold the fastest position in all cases.
Its major strengths include its competitive speeds,
Unix-style pipes,
paired-end handling,
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