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MashMap is an approximate algorithm for computing local alignment boundaries between long DNA sequences. Given a minimum alignment length and an identity threshold, it computes the desired alignment boundaries and identity estimates using kmer-based statistics, and maintains sufficient probabilistic guarantees on the output sensitivity.

Reference:

• Chirag Jain, Sergey Koren, Alexander Dilthey, Adam M. Phillippy, Srinivas Aluru
  A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps
  Bioinformatics, 2018, 34(17): i748-i756; doi: 10.1093/bioinformatics/bty597

• MashMap GitHub page

• Module Name: MashMap (see the modules page for more information)
• Unusual environment variables set
  • MASHMAP_BIN       executable directory
  • MASHMAP_SRC       source code directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=8g --cpus-per-task=16
[user@cn3200 ~]$module load MashMap 
[+] Loading GSL 2.5 for GCC 7.2.0 ... 
[+] Loading MashMap  2.0 
[user@cn3200 ~]$ mashmap -h
-----------------
Mashmap is an approximate long read or contig mapper based on Jaccard
similarity
-----------------
Example usage:
$ mashmap -r ref.fa -q seq.fq [OPTIONS]
$ mashmap --rl reference_files_list.txt -q seq.fq [OPTIONS]

Available options
-----------------
-h, --help
    Print this help page

-r , --ref 
    an input reference file (fasta/fastq)[.gz]

--refList , --rl 
    a file containing list of reference files, one per line

-q , --query 
    an input query file (fasta/fastq)[.gz]

--ql , --queryList 
    a file containing list of query files, one per line

...

-t , --threads 
    count of threads for parallel execution [default : 1]

-o , --output 
    output file name [default : mashmap.out]
...

Download testing data from the PacBio's release of Human 54x long-read coverage dataset
(http://datasets.pacb.com/2014/Human54x/fastq.html ):

[user@cn3200 ~]$ wget http://datasets.pacb.com/2013/Human10x/READS/2530572/0001/Analysis_Results/m130929_024849_42213_c100518541910000001823079209281311_s1_p0.1.subreads.fastq -O test_seq.fq

--2019-01-10 12:08:07--  http://datasets.pacb.com/2013/Human10x/READS/2530572/0001/Analysis_Results/m130929_024849_42213_c100518541910000001823079209281311_s1_p0.1.subreads.fastq
Resolving dtn04-e0 (dtn04-e0)... 10.1.200.240
Connecting to dtn04-e0 (dtn04-e0)|10.1.200.240|:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 361764079 (345M) [application/octet-stream]
Saving to: ‘test_seq.fq’

100%[===============================================================>] 361,764,079 96.8MB/s   in 3.6s

2019-01-10 12:08:11 (96.2 MB/s) - ‘test_seq.fq’ saved [361764079/361764079]

Specify a human reference GRCh38 sequence:

[user@cn3200 ~]$ ln -s /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa human_GRCh38.fa

Run the software on these data with 16 threads:

[user@cn3200 ~]$ mashmap -r human_GRCh38.fa -q test_seq.fq -t 16
>>>>>>>>>>>>>>>>>>
Reference = [human_GRCh38.fa]
Query = [test_seq.fq]
Kmer size = 16
Window size = 111
Segment length = 5000 (read split allowed)
Alphabet = DNA
Percentage identity threshold = 85%
Mapping output file = mashmap.out
Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
Execution threads  = 16
>>>>>>>>>>>>>>>>>>
INFO, skch::Sketch::build, minimizers picked from reference = 52513331
INFO, skch::Sketch::index, unique minimizers = 17607584
INFO, skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 9361370) ... (116827, 1)
INFO, skch::Sketch::computeFreqHist, With threshold 0.001%, ignore minimizers occurring >= 5534 times during lookup.
INFO, skch::main, Time spent computing the reference index: 58.0907 sec
INFO, skch::Map::mapQuery, [count of mapped reads, reads qualified for mapping, total input reads] = [11978, 13497, 25249]
INFO, skch::main, Time spent mapping the query : 21.6042 sec
INFO, skch::main, mapping results saved in : mashmap.out

The result will be stored in the file 'mashmap.out'.

End the interactive session:

[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$