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@@ -1322,7 +1322,7 @@ <h3 id="reproducibility">Reproducibility</h3> | |
| <h2 id="seqkit">seqkit</h2> | ||
| <pre><code class="language-text">SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation | ||
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| Version: 2.8.0 | ||
| Version: 2.9.0 | ||
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| Author: Wei Shen <[email protected]> | ||
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@@ -1873,6 +1873,7 @@ <h2 id="stats">stats</h2> | |
| 16. Q30(%) percentage of bases with the quality score greater than 30 | ||
| 17. AvgQual average quality | ||
| 18. GC(%) percentage of GC content | ||
| 19. sum_n number of ambitious letters (N, n, X, x) | ||
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| Attention: | ||
| 1. Sequence length metrics (sum_len, min_len, avg_len, max_len, Q1, Q2, Q3) | ||
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@@ -2020,13 +2021,13 @@ <h2 id="stats">stats</h2> | |
| <li> | ||
| <p>Extra information</p> | ||
| <pre><code>$ seqkit stats *.f{a,q}.gz -a | ||
| file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%) | ||
| hairpin.fa.gz FASTA RNA 28,645 2,949,871 39 103 2,354 76 91 111 0 101 380 0 0 0 45.77 | ||
| mature.fa.gz FASTA RNA 35,828 781,222 15 21.8 34 21 22 22 0 22 12 0 0 0 47.6 | ||
| Illimina1.8.fq.gz FASTQ DNA 10,000 1,500,000 150 150 150 150 150 150 0 150 1 96.16 89.71 24.82 49.91 | ||
| nanopore.fq.gz FASTQ DNA 4,000 1,798,723 153 449.7 6,006 271 318 391 0 395 585 40.79 12.63 9.48 46.66 | ||
| reads_1.fq.gz FASTQ DNA 2,500 567,516 226 227 229 227 227 227 0 227 3 91.24 86.62 15.45 53.63 | ||
| reads_2.fq.gz FASTQ DNA 2,500 560,002 223 224 225 224 224 224 0 224 2 91.06 87.66 14.62 54.77 | ||
| file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%) sum_n | ||
| hairpin.fa.gz FASTA RNA 28,645 2,949,871 39 103 2,354 76 91 111 0 101 380 0 0 0 45.77 255 | ||
| mature.fa.gz FASTA RNA 35,828 781,222 15 21.8 34 21 22 22 0 22 12 0 0 0 47.6 0 | ||
| Illimina1.8.fq.gz FASTQ DNA 10,000 1,500,000 150 150 150 150 150 150 0 150 1 96.16 89.71 24.82 49.91 38 | ||
| nanopore.fq.gz FASTQ DNA 4,000 1,798,723 153 449.7 6,006 271 318 391 0 395 585 40.79 12.63 9.48 46.66 0 | ||
| reads_1.fq.gz FASTQ DNA 2,500 567,516 226 227 229 227 227 227 0 227 3 91.24 86.62 15.45 53.63 44 | ||
| reads_2.fq.gz FASTQ DNA 2,500 560,002 223 224 225 224 224 224 0 224 2 91.06 87.66 14.62 54.77 2 | ||
| </code></pre> | ||
| </li> | ||
| <li> | ||
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@@ -4274,7 +4275,9 @@ <h2 id="replace">replace</h2> | |
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| Special replacement symbols (only for replacing name not sequence): | ||
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| {nr} Record number, starting from 1 | ||
| {fn} File name | ||
| {fbn} File base name | ||
| {fbne} File base name without any extension | ||
| {kv} Corresponding value of the key (captured variable $n) by key-value file, | ||
| n can be specified by flag -I (--key-capt-idx) (default: 1) | ||
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@@ -4425,6 +4428,14 @@ <h2 id="replace">replace</h2> | |
| </code></pre> | ||
| </li> | ||
| <li> | ||
| <p>Add file names.</p> | ||
| <pre><code>$ seqkit replace ../tests/hairpin.fa -p '.+' -r '{fn}__{fbn}__{fbne}__{nr}' | seqkit seq -n | head -n 3 | ||
| ../tests/hairpin.fa__hairpin.fa__hairpin__1 | ||
| ../tests/hairpin.fa__hairpin.fa__hairpin__2 | ||
| ../tests/hairpin.fa__hairpin.fa__hairpin__3 | ||
| </code></pre> | ||
| </li> | ||
| <li> | ||
| <p>Replace key with value by key-value file</p> | ||
| <pre><code>$ more test.fa | ||
| >seq1 name1 | ||
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