LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, viral, or long-read sequences against up to millions of prokaryotic genomes.
Documents: https://bioinf.shenwei.me/LexicMap
Preprint:
Wei Shen and Zamin Iqbal. (2024) LexicMap: efficient sequence alignment against millions of prokaryotic genomes. bioRxiv. https://doi.org/10.1101/2024.08.30.610459
- LexicMap is scalable to up to millions of prokaryotic genomes.
- The sensitivity of LexicMap is comparable with Blastn.
- The alignment is fast and memory-efficient.
- LexicMap is easy to install, we provide binary files with no dependencies for Linux, Windows, MacOS (x86 and arm CPUs).
- LexicMap is easy to use (tutorials and usages). Both tabular and Blast-style output formats are available.
- Besides, we provide several commands to explore the index data and extract indexed subsequences.
Motivation: Alignment against a database of genomes is a fundamental operation in bioinformatics, popularised by BLAST. However, given the increasing rate at which genomes are sequenced, existing tools struggle to scale.
- Existing full alignment tools face challenges of high memory consumption and slow speeds.
- Alignment-free large-scale sequence searching tools only return the matched genomes, without the vital positional information for downstream analysis.
- Prefilter+Align strategies have the sensitivity issue in the prefiltering step.
Methods: (algorithm overview)
- An improved version of the sequence sketching method LexicHash is adopted to compute alignment seeds accurately and efficiently.
- We solved the sketching deserts problem of LexicHash seeds to provide a window guarantee.
- We added the support of suffix matching of seeds, making seeds much more tolerant to mutations. Any 31-bp seed with a common ≥15 bp prefix or suffix can be matched, which means seeds are immune to any single SNP.
- A hierarchical index enables fast and low-memory variable-length seed matching (prefix + suffix matching).
- A pseudo alignment algorithm is used to find similar sequence regions from chaining results for alignment.
- A reimplemented Wavefront alignment algorithm is used for base-level alignment.
Results:
-
LexicMap enables efficient indexing and searching of both RefSeq+GenBank and the AllTheBacteria datasets (2.3 and 1.9 million prokaryotic assemblies respectively). Running at this scale has previously only been achieved by Phylign (previously called mof-search), which compresses genomes with phylogenetic information and provides searching (prefiltering with COBS and alignment with minimap2).
-
For searching in all 2,340,672 Genbank+Refseq prokaryotic genomes, Blastn is unable to run with this dataset on common servers as it requires >2000 GB RAM. (see performance).
With LexicMap (48 CPUs),
Query Genome hits Time RAM A 1.3-kb marker gene 37,164 36 s 4.1 GB A 1.5-kb 16S rRNA 1,949,496 10 m 41 s 14.1 GB A 52.8-kb plasmid 544,619 19 m 20 s 19.3 GB 1003 AMR genes 25,702,419 187 m 40 s 55.4 GB
More documents: https://bioinf.shenwei.me/LexicMap.
Building an index (see the tutorial of building an index).
# From a directory with multiple genome files
lexicmap index -I genomes/ -O db.lmi
# From a file list with one file per line
lexicmap index -X files.txt -O db.lmi
Querying (see the tutorial of searching).
# For short queries like genes or long reads, returning top N hits.
lexicmap search -d db.lmi query.fasta -o query.fasta.lexicmap.tsv \
--min-qcov-per-hsp 70 --min-qcov-per-genome 70 --top-n-genomes 1000
# For longer queries like plasmids, returning all hits.
lexicmap search -d db.lmi query.fasta -o query.fasta.lexicmap.tsv \
--min-qcov-per-hsp 0 --min-qcov-per-genome 0 --top-n-genomes 0
Sample output (queries are a few Nanopore Q20 reads). See output format details.
query qlen hits sgenome sseqid qcovGnm hsp qcovHSP alenHSP pident gaps qstart qend sstart send sstr slen
------------------ ---- ---- --------------- ------------- ------- --- ------- ------- ------- ---- ------ ---- ------- ------- ---- -------
ERR5396170.1000016 740 1 GCF_013394085.1 NZ_CP040910.1 89.595 1 89.595 663 99.246 0 71 733 13515 14177 + 1887974
ERR5396170.1000000 698 1 GCF_001457615.1 NZ_LN831024.1 85.673 1 85.673 603 98.010 5 53 650 4452083 4452685 + 6316979
ERR5396170.1000017 516 1 GCF_013394085.1 NZ_CP040910.1 94.574 1 94.574 489 99.591 2 27 514 293509 293996 + 1887974
ERR5396170.1000012 848 1 GCF_013394085.1 NZ_CP040910.1 95.165 1 95.165 811 97.411 7 22 828 190329 191136 - 1887974
ERR5396170.1000038 1615 1 GCA_000183865.1 CM001047.1 64.706 1 60.000 973 95.889 13 365 1333 88793 89756 - 2884551
ERR5396170.1000038 1615 1 GCA_000183865.1 CM001047.1 64.706 2 4.706 76 98.684 0 266 341 89817 89892 - 2884551
ERR5396170.1000036 1159 1 GCF_013394085.1 NZ_CP040910.1 95.427 1 95.427 1107 99.729 1 32 1137 1400097 1401203 + 1887974
ERR5396170.1000031 814 4 GCF_013394085.1 NZ_CP040910.1 86.486 1 86.486 707 99.151 3 104 807 242235 242941 - 1887974
ERR5396170.1000031 814 4 GCF_013394085.1 NZ_CP040910.1 86.486 2 86.486 707 98.444 3 104 807 1138777 1139483 + 1887974
ERR5396170.1000031 814 4 GCF_013394085.1 NZ_CP040910.1 86.486 3 84.152 688 98.983 4 104 788 154620 155306 - 1887974
ERR5396170.1000031 814 4 GCF_013394085.1 NZ_CP040910.1 86.486 4 84.029 687 99.127 3 104 787 32477 33163 + 1887974
ERR5396170.1000031 814 4 GCF_013394085.1 NZ_CP040910.1 86.486 5 72.727 595 98.992 3 104 695 1280183 1280777 + 1887974
ERR5396170.1000031 814 4 GCF_013394085.1 NZ_CP040910.1 86.486 6 11.671 95 100.000 0 693 787 1282480 1282574 + 1887974
ERR5396170.1000031 814 4 GCF_013394085.1 NZ_CP040910.1 86.486 7 82.064 671 99.106 3 120 787 1768782 1769452 + 1887974
CIGAR string, aligned query and subject sequences can be outputted as extra columns via the flag -a/--all.
# Extracting similar sequences for a query gene.
# search matches with query coverage >= 90%
lexicmap search -d gtdb_complete.lmi/ b.gene_E_faecalis_SecY.fasta -o results.tsv \
--min-qcov-per-hsp 90 --all
# extract matched sequences as FASTA format
sed 1d results.tsv | awk -F'\t' '{print ">"$5":"$14"-"$15":"$16"\n"$20;}' \
| seqkit seq -g > results.fasta
seqkit head -n 1 results.fasta | head -n 3
>NZ_JALSCK010000007.1:39224-40522:-
TTGTTCAAGCTATTAAAGAACGCCTTTAAAGTCAAAGACATTAGATCAAAAATCTTATTT
ACAGTTTTAATCTTGTTTGTATTTCGCCTAGGTGCGCACATTACTGTGCCCGGGGTGAAT
Export blast-style format:
seqkit seq -M 500 q.long-reads.fasta.gz \
| seqkit head -n 1 \
| lexicmap search -d demo.lmi/ -a \
| lexicmap utils 2blast --kv-file-genome ass2species.map
Query = GCF_006742205.1_r100
Length = 431
[Subject genome #1/1] = GCF_006742205.1 Staphylococcus epidermidis
Query coverage per genome = 92.575%
>NZ_AP019721.1
Length = 2422602
HSP #1
Query coverage per seq = 92.575%, Aligned length = 402, Identities = 98.507%, Gaps = 4
Query range = 33-431, Subject range = 1321677-1322077, Strand = Plus/Minus
Query 33 TAAAACGATTGCTAATGAGTCACGTATTTCATCTGGTTCGGTAACTATACCGTCTACTAT 92
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1322077 TAAAACGATTGCTAATGAGTCACGTATTTCATCTGGTTCGGTAACTATACCGTCTACTAT 1322018
Query 93 GGACTCAGTGTAACCCTGTAATAAAGAGATTGGCGTACGTAATTCATGTG-TACATTTGC 151
|||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct 1322017 GGACTCAGTGTAACCCTGTAATAAAGAGATTGGCGTACGTAATTCATGTGATACATTTGC 1321958
Query 152 TATAAAATCTTTTTTCATTTGATCAAGATTATGTTCATTTGTCATATCACAGGATGACCA 211
|||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct 1321957 TATAAAATCTTTTTTCATTTGATCAAGATTATGTTCATTTGTCATATCAC-GGATGACCA 1321899
Query 212 TGACAATACCACTTCTACCATTTGTTTGAATTCTATCTATATAACTGGAGATAAATACAT 271
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1321898 TGACAATACCACTTCTACCATTTGTTTGAATTCTATCTATATAACTGGAGATAAATACAT 1321839
Query 272 AGTACCTTGTATTAATTTCTAATTCTAA-TACTCATTCTGTTGTGATTCAAATGGTGCTT 330
|||||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||
Sbjct 1321838 AGTACCTTGTATTAATTTCTAATTCTAAATACTCATTCTGTTGTGATTCAAATGTTGCTT 1321779
Query 331 CAATTTGCTGTTCAATAGATTCTTTTGAAAAATCATCAATGTGACGCATAATATAATCAG 390
|||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct 1321778 CAATTTGCTGTTCAATAGATTCTTTTGAAAAATCATCAATGTGACGCATAATATCATCAG 1321719
Query 391 CCATCTTGTT-GACAATATGATTTCACGTTGATTATTAATGC 431
|||||||||| |||||||||||||||||||||||||||||||
Sbjct 1321718 CCATCTTGTTTGACAATATGATTTCACGTTGATTATTAATGC 1321677
Learn more tutorials and usages.
See performance.
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
We also provide pre-release binaries, with new features and improvements.
Wei Shen and Zamin Iqbal. (2024) LexicMap: efficient sequence alignment against millions of prokaryotic genomes. bioRxiv. https://doi.org/10.1101/2024.08.30.610459
- In the LexicMap source code and command line options, the term "mask" is used, following the terminology in the LexicHash paper.
- In the LexicMap manuscript, however, we use "probe" as it is easier to understand. Because these masks, which consist of thousands of k-mers and capture k-mers from sequences through prefix matching, function similarly to DNA probes in molecular biology.
Please open an issue to report bugs, propose new functions or ask for help.
- High-performance LexicHash computation in Go.
- Wavefront alignment algorithm (WFA) in Golang.
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