![]() ![]() The Parallelization is implemented by multiple goroutines in golang The pgzip package reads and write gzip files in parallel. Parsing of line-based files, including BED/GFF file and ID list file are also parallelized. The validation of sequences bases and complement process of sequences SeqKit uses full sequence head instead of just ID as key. seqkit.fai file created by SeqKit is a little different from. Rapid access of sequences and reducing memory occupation.ĪTTENTION: the. When input files are (plain or gzipped) FASTA files, FASTA indexįor some commands, including subseq, split, sort and shuffle, The gi number, then use -id-regexp "^gi\|(+)\|". id-regexp "\|(+)\| " or just use flag -id-ncbi. In this case, we could set sequence ID parsing regular expression by global flag Seqkit accepts input data from standard input (STDIN) and plain or gzip-compressed files.įiles can be given via positional arguments or the flag -infile-list. seqtk+pigz: seqtk pipes data to the multithreaded pigz which uses 4 threads here.seqtk+gzip: seqtk pipes data to the single-threaded gzip.SeqKit uses the author's lightweight and high-performance bioinformatics package Seqkit also supports reading and writing xz (.xz) and zstd (.zst) formats since v2.2.0. Technical details and guides for use FASTA/Q format parsing and writing Edit: concat, replace, restart, mutate,.Searching: grep, locate, amplicon, fish.Format conversion: fq2fa, fa2fq, fx2tab, tab2fx,.Basic: seq, stats, sum, subseq, sliding,. ![]()
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