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FastA index (.fai) handler compatible with samtools faidx. .fai is extended with 4 columns storing counts for A, C, G & T for each sequence.



  • Python 2.7


-h, --help

show this help message and exit


show program’s version number and exit

-v, --verbose


-i FASTA, --fasta FASTA

FASTA file(s)

-o OUT, --out OUT

output stream [stdout]

-r REGIONS, --regions REGIONS

contig(s) or contig region(s) to output (returns reverse complement if end larger than start)

-N N

calculate NXX and exit ie N50

-L L

calculate LXX and exit ie L50

-S, --stats

return FastA stats aka fasta_stats


# retrieve sequence of scaffold00001 starting at 100 and ending at 200 base (0-based)
FastaIndex -i contigs.fa -r 'scaffold00001:100-200'

# retrieve reverse complement of the same region
FastaIndex -i contigs.fa -r 'scaffold00001:200-100'

# calculate N50 of FastA file
FastaIndex -i contigs.fa -N50

# more statistics of FastA file
FastaIndex -i contigs.fa -S
# or
fasta_stats -i contigs.fa


sudo pip install -U FastaIndex

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