LexicMap

LexicMap

LexicMap: efficient sequence alignment against millions of microbial genomes​.

Quick start

Building an index

# from a directory
lexicmap index -I genomes/ -O db.lmi --force \
    -k 31 --masks 10000

# from a file list
lexicmap index -X files.txt -S -O db.lmi --force \
    -k 31 --masks 10000

Querying

lexicmap search -d db.lmi query.fasta -o query.fasta.txt \
    --min-aligned-fraction 60 --min-identity 60

Sample output

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 query    qlen   refs   ref               seqid           afrac    ident       tlen    tstart      tend   strand   seeds
-------------------------------------------------------------------------------------------------------------------------
 read_1    333    1     GCF_013394085.1   NZ_CP040910.1   86.486   87.847   1887974    196495    196827     -        2
 read_2    578    1     GCF_013394085.1   NZ_CP040910.1   87.024   98.211   1887974   1709172   1709749     +        3
 read_3    297    1     GCF_013394085.1   NZ_CP040910.1   73.401   99.083   1887974   1879531   1879827     +        1
 read_4    586    1     GCF_013394085.1   NZ_CP040910.1   84.642   89.718   1887974   1624549   1625134     +        1
 read_5    749    1     GCF_000392875.1   NZ_KB944589.1   89.987   91.691    682426    342117    342866     +        2
 read_6    699    1     GCF_013394085.1   NZ_CP040910.1   79.542   94.784   1887974     38079     38776     +        3
 read_7   1779    1     GCF_013394085.1   NZ_CP040910.1   96.684   93.372   1887974   1622969   1624753     -        5
 read_8   3139    3     GCF_000307025.1   NC_018584.1     82.606   93.868   2951805    126520    129674     -        6
 read_8   3139    3     GCF_900187225.1   NZ_LT906436.1   80.917   83.504   2864663    112898    116051     -        5
 read_8   3139    3     GCF_013282665.1   NZ_CP054041.1   75.852   77.908   2788056   1295185   1298323     -        2
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Installation

LexicMap is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page.

Or install with conda:

conda install -c bioconda lexicmap

Related projects

• High-performance LexicHash computation in Go.

Support

Please open an issue to report bugs, propose new functions or ask for help.

License

MIT License