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Category,Command,Function,Input,Strand-sensitivity,Multi-threads
Basic operation,[seq](https://bioinf.shenwei.me/seqkit/usage/#seq),"Transform sequences: extract ID/seq, filter by length/quality, remove gaps…",FASTA/Q,,
,[stats](https://bioinf.shenwei.me/seqkit/usage/#stats),"Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%…",FASTA/Q,,✓
,[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq),"Get subsequences by region/gtf/bed, including flanking sequences",FASTA/Q,+ or/and -,
,[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding),Extract subsequences in sliding windows,FASTA/Q,+ only,
,[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx),Create the FASTA index file and extract subsequences (with more features than samtools faidx),FASTA,+ or/and -,
,[translate](https://bioinf.shenwei.me/seqkit/usage/#translate),translate DNA/RNA to protein sequence,FASTA/Q,+ or/and -,
,[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ),Monitoring and online histograms of sequence features,FASTA/Q,,
,[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ),Real time concatenation and streaming of fastx files,FASTA/Q,,✓
Format conversion,[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa),Convert FASTQ to FASTA format,FASTQ,,
,[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab),Convert FASTA/Q to tabular format,FASTA/Q,,
,[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq),Retrieve corresponding FASTQ records by a FASTA file,FASTA/Q,+ only,
,[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx),Convert tabular format to FASTA/Q format,TSV,,
,[convert](https://bioinf.shenwei.me/seqkit/usage/#convert),"Convert FASTQ quality encoding between Sanger, Solexa and Illumina",FASTA/Q,,
Searching,[grep](https://bioinf.shenwei.me/seqkit/usage/#grep),"Search sequences by ID/name/sequence/sequence motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m"
,[locate](https://bioinf.shenwei.me/seqkit/usage/#locate),"Locate subsequences/motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m"
,[amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon),"Extract amplicon (or specific region around it), mismatch allowed",FASTA/Q,+ and -,"partly, -m"
,[fish](https://bioinf.shenwei.me/seqkit/usage/#fish),Look for short sequences in larger sequences,FASTA/Q,+ and -,
Set operation,[sample](https://bioinf.shenwei.me/seqkit/usage/#sample),Sample sequences by number or proportion,FASTA/Q,,
,[rmdup](https://bioinf.shenwei.me/seqkit/usage/#rmdup),Remove duplicated sequences by ID/name/sequence,FASTA/Q,+ and -,
,[common](https://bioinf.shenwei.me/seqkit/usage/#common),Find common sequences of multiple files by id/name/sequence,FASTA/Q,+ and -,
,[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate),Duplicate sequences N times,FASTA/Q,,
,[split](https://bioinf.shenwei.me/seqkit/usage/#split),Split sequences into files by id/seq region/size/parts (mainly for FASTA),FASTA preffered,,
,[split2](https://bioinf.shenwei.me/seqkit/usage/#split2),"Split sequences into files by size/parts (FASTA, PE/SE FASTQ)",FASTA/Q,,
,[head](https://bioinf.shenwei.me/seqkit/usage/#head),Print first N FASTA/Q records,FASTA/Q,,
,[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome),Print sequences of the first genome with common prefixes in name,FASTA/Q,,
,[range](https://bioinf.shenwei.me/seqkit/usage/#range),Print FASTA/Q records in a range (start:end),FASTA/Q,,
,[pair](https://bioinf.shenwei.me/seqkit/usage/#pair),Patch up paired-end reads from two fastq files,FASTA/Q,,
Edit,[replace](https://bioinf.shenwei.me/seqkit/usage/#replace),Replace name/sequence by regular expression,FASTA/Q,+ only,
,[rename](https://bioinf.shenwei.me/seqkit/usage/#rename),Rename duplicated IDs,FASTA/Q,,
,[concat](https://bioinf.shenwei.me/seqkit/usage/#concat),Concatenate sequences with same ID from multiple files,FASTA/Q,+ only,
,[restart](https://bioinf.shenwei.me/seqkit/usage/#restart),Reset start position for circular genome,FASTA/Q,+ only,
,[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate),"Edit sequence (point mutation, insertion, deletion)",FASTA/Q,+ only,
,[sana](https://bioinf.shenwei.me/seqkit/usage/#sana),Sanitize broken single line FASTQ files,FASTQ,,
Ordering,[sort](https://bioinf.shenwei.me/seqkit/usage/#sort),Sort sequences by id/name/sequence/length,FASTA preffered,,
,[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle),Shuffle sequences,FASTA preffered,,
BAM processing,[bam](https://bioinf.shenwei.me/seqkit/usage/#bam),Monitoring and online histograms of BAM record features,BAM,,
Miscellaneous,[sum](https://bioinf.shenwei.me/seqkit/usage/#sum),Compute message digest for all sequences in FASTA/Q files,FASTA/Q,,✓
,[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides),Merge sliding windows generated from seqkit sliding,TSV,,
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