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<p>Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. <strong><em>iMeta</em></strong> e191. <ahref="https://doi.org/10.1002/imt2.191">doi:10.1002/imt2.191</a>.
<li>add flags to specify sequences to operate/transform. <ahref="https://github.com/shenwei356/seqkit/issues/568">#568</a></li>
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</ul>
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</li>
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<li><code>seqkit split2</code>:<ul>
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<li>add a new flag <code>-N, --seqid-as-filename</code> to use the first sequence ID as the file name.
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E.g., using <code>-N -s 1</code> is equal to <code>seqkit split --by-id</code>, but it's much faster and uses less memory.</li>
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<li><code>seqkit shuffle</code>:<ul>
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<li>add a new option <code>--tmp-dir</code>, which can specify tmp dir for FASTA records from stdin or compressed FASTA files. <ahref="https://github.com/shenwei356/seqkit/issues/562">#562</a></li>
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</ul>
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</li>
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<li><code>seqkit head</code>:<ul>
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<li>add a new flag <code>-l, --length</code> to print heading FASTA/Q records with total sequence length >= N, e.g., <code>-l 2G</code>.</li>
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<li><code>seqkit shuffle/sample</code>:<ul>
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<li>add a new flag <code>-r/--non-deterministic</code>, which uses a time-based seed to <strong>generate non-deterministic (truly random) results</strong>. <ahref="https://github.com/shenwei356/seqkit/issues/565">#565</a></li>
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</ul>
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</li>
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<li><code>seqkit replace</code>:<ul>
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<li>add a new replacement symbol <code>{uuid}</code> for random UUID. <ahref="https://github.com/shenwei356/seqkit/issues/552">#552</a></li>
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<li><code>seqkit restart</code>:<ul>
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<li><strong>support specifying the starting sequence of circular genomes</strong>.</li>
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</ul>
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</li>
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<li><code>seqkit split/split2</code>:<ul>
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<li>add a new option <code>-P/--out-prefix</code> to override <code>--by-*-prefix</code>, for simplifying output prefix setting. <ahref="https://github.com/shenwei356/seqkit/issues/563">#563</a></li>
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</ul>
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</li>
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<li><code>seqkit bam</code>:<ul>
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<li>fix a bug <ahref="https://github.com/shenwei356/seqkit/issues/200">#200</a> by @botond-sipos.</li>
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</ul>
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</li>
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<li><code>seqkit stats</code>:<ul>
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<li>fix detecting file format type for FASTQ records with empty sequences. <ahref="https://github.com/shenwei356/seqkit/issues/569">#569</a></li>
<li><code>-p/--pattern</code> accepts empty character (<code>""</code>) now. So it's able to <strong>search records with empty IDs or sequences</strong>. <ahref="https://github.com/shenwei356/seqkit/issues/558">#558</a></li>
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</ul>
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</li>
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<li><code>seqkit split2</code>:<ul>
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<li>fix a bug introduced in v2.11.0: <code>--by-part-prefix</code> options has no effect. <ahref="https://github.com/shenwei356/seqkit/issues/554">#554</a></li>
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</ul>
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</li>
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<li><code>seqkit replace</code>:<ul>
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<li><code>{uuid}</code>: use the time-sortable UUIDv7 to replace v4.</li>
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</ul>
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</li>
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<li><code>seqkit stats/fx2tab</code>:<ul>
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<li>add information about how the average quality is computed. <ahref="https://github.com/shenwei356/seqkit/issues/448">#448</a></li>
<li>Ultrafast (see <ahref="http://bioinf.shenwei.me/seqkit/usage/#technical-details-and-guides-for-use">technical-details</a> and <ahref="http://bioinf.shenwei.me/seqkit/benchmark">benchmark</a>)</li>
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<li>Seamlessly parsing both FASTA and FASTQ formats</li>
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<li>Supporting (<code>gzip</code>/<code>xz</code>/<code>zstd</code>/<code>bzip2</code> compressed) STDIN/STDOUT and input/output file, easily integrated in pipe</li>
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<li>Supporting (<code>gzip</code>/<code>xz</code>/<code>zstd</code>/<code>bzip2</code>/<code>lz4</code> compressed) STDIN/STDOUT and input/output file, easily integrated in pipe</li>
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<li>Reproducible results (configurable rand seed in <code>sample</code> and <code>shuffle</code>)</li>
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<li>Supporting custom sequence ID via regular expression</li>
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