Table 2:

List of commands included in both BigSeqKit and seqkit. Those commands with an asterisk support new functionalities not included in seqkit

Basic commands
seq	Transform sequences (extract ID, filter by length, remove gaps, reverse complement, etc.)
subseq	Get subsequences by region/gtf/bed, including flanking sequences
stats	Simple statistics of FASTA/Q files: #seqs, min/max length, N50, Q20%, Q30%, etc.
faidx*	Create FASTA or FASTQ index file and extract subsequences
Format conversion
fa2fq	Retrieve corresponding FASTQ records by a FASTA file
fq2fa	Convert FASTQ file to FASTA format
translate	Translate DNA/RNA to protein sequence
Searching
grep	Search sequences by ID/name/sequence/sequence motifs
locate	Locate subsequences/motifs
Set operations
sample	Sample sequences by number or proportion
rmdup	Remove duplicated sequences by ID/name/sequence
common	Find common sequences of multiple files by ID/name/sequence
duplicate	Duplicate sequences N times
head	Print first N FASTA/Q records
head-genome	Print sequences of the first genome with common prefixes in name
pair	Match up paired-end reads from 2 FASTQ files
range	Print FASTA/Q records in a range (start:end)
Edit
concat	Concatenate sequences with the same ID from multiple files
replace	Replace name/sequence using a regular expression
rename	Rename duplicated IDs
Ordering
sort	Sort sequences by ID/name/sequence/length
shuffle	Shuffle sequences