fastutils
Quick start
# check number of reads, number of bases, and base composition of a fasta/q file
fastutils stat -i reads.fastq
# check mean read length
fastutils length -i reads.fastq | datamash mean 1
# convert fastq to fasta
fastutils format -i reads.fastq > reads.fasta
# print reads longer than 1000 bp and format in lines of length 60 bp
fastutils format -i reads.fastq -m 1000 -w 60 > reads.1000.fasta
# interleave paired-end dataset
fastutils interleave -1 reads_1.fastq -2 reads_2.fastq -q > reads.fastq
# subsample 25x coverage of reads randomly (assuming E.coli dataset)
fastutils subsample -i reads.fastq -d 25 -g 4.6m -r > reads.subsample.fasta
# print first 1 million bp of chr1 and format in lines of length 60 bp
fastutils subseq -i hg38.fa -o - chr1:0-1000000 | fastutils format -w 60 > chr1.chunk.fasta
# compare each sequences with its reverse complement and print lexicographically smaller one
fastutils revcomp -i reads.fastq -l > reads.lex.fasta
# piping example; Get all contigs of chrX
cat hg38.fa | fastutils format | grep ">chrX" -A1 | fastutils cutN -i - > chrX.contigs.faAvailable commands
stat prints general statistics of fasta/q files
length prints read ids and their length in tabular format
format re-formats the fasta/q file based on user's needs
interleave generate interleave paired end reads
revcomp prints the reverse complement of each sequence
subsample output a fraction of reads depending on the desired coverage
subseq extracts a subsequence from the fasta/q file
cutN breaks fasta entries into contigs (if containing N's)
For details about each command enter fastutils <command> -h.
Command details
fastutils stat
Reports the number of reads, number of bases, and base composition of the input FASTA/Q file.
Usage: fastutils stat [options]
I/O options:
-i,--in STR input file in fasta/q format [stdin]
-o,--out STR output file [stdout]
More options:
-m,--minLen INT min read length [0]
-M,--maxLen INT max read length [INT64_MAX]
-h,--help print this help
fastutils length
Prints the name and length of each read (separated by tab), one read per line.
Usage: fastutils length [options]
I/O options:
-i,--in STR input file in fasta/q format [stdin]
-o,--out STR output file [stdout]
More options:
-m,--minLen INT min read length [0]
-M,--maxLen INT max read length [LLONG_MAX]
-t,--total print total number of bases in third column
-h,--help print this help
fastutils format
Change the format of the input file.
Usage: fastutils format [options]
I/O options:
-i,--in STR input file in fasta/q format [stdin]
-o,--out STR output file [stdout]
More options:
-w,--lineWidth INT size of lines in fasta output. Use 0 for no wrapping [0]
-m,--minLen INT min read length [0]
-M,--maxLen INT max read length [LLONG_MAX]
-q,--fastq output reads in fastq format if possible
-n,--noN do not print entries with N's
-c,--comment print comments in headers
-d,--digital use read index instead as read name
-k,--keep keep name as a comment when using -d
-p,--prefix STR prepend STR to the name
-s,--suffix STR append STR to the name
-P,--pacbio use pacbio's header format
-h,--help print this help
fastutils interleave
Takes two fasta/q files of one or multiple paired-end/mate-pair library and print the sequences in interleaved/interlaced format.
Usage: fastutils interleave [options] -1 lib1_1.fq -2 lib1_2.fq [-1 lib2_1.fq -2 lib2_2.fq ...]
I/O options:
-1,--in1 STR fasta/q file containing forward (left) reads [required]
-2,--in2 STR fasta/q file containing reverse (right) reads [required]
-o,--out STR output interlaced reads in STR file [stdout]
More options:
-q,--fastq output reads in fastq format if possible
-s,--separator CHR separator character [.]
-h,--help print this help
fastutils revcomp
Print the reverse complement of the sequences contained in the input.
Usage: fastutils revcomp [options]
I/O options:
-i,--in STR input file in fasta/q format [stdin]
-o,--out STR output file [stdout]
More options:
-w,--lineWidth INT size of lines in fasta output. Use 0 for no wrapping [0]
-q,--fastq output reads in fastq format if possible
-c,--comment print comments in headers
-l,--lex output lexicographically smaller sequence
-h,--help print this help
fastutils subsample
Downsamples the input file to a desired depth of coverage. User can choose to select random reads, longest reads, or from top (default).
Usage: fastutils subsample -i input -d depth -g genomeSize
I/O options:
-i,--in STR input file in fasta/q format. This options is required if -r or -l are used [stdin]
-o,--out STR output file [stdout]
More options:
-d,--depth INT coverage of the subsampled set [required]
-g,--genomeSize FLT length of the genome. Accepted suffixes are k,m,g [required]
-r,--random subsample randomly instead of selecting top reads
-l,--longest subsample longest reads instead of selecting top reads
-s,--seed INT seed for random number generator
-q,--fastq output reads in fastq format if possible
-c,--comment print comments in headers
-n,--num use read index instead of read name
-k,--keep keep name as a comment when using -n
-h,--help print this help
fastutils subseq
Extracts desired subsequences from input file.
Usage: fastutils subseq [options] <name:start-end> [<name2:start2-end2> ...]
Required options:
-i STR input file in fastx format. Use - for stdin.
-o STR output file. Use - for stdout.
More options:
-v print version and build date
-h print this help
fastutils cutN
Cuts fasta entries at N bases. This is useful for converting scaffolds to contigs.
Usage: fastutils cutN [options]
Required options:
-i STR input file in fastx format. Use - for stdin.
-o STR output file in fasta format. Use - for stdout.
More options:
-v print version and build date
-h print this help
Bug report
Please report the bugs through issue tracker at https://github.com/haghshenas/fastutils/issues.
Copyright and License
This software is released under GNU General Public License (v3.0)
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