syncmer

Validation of sycnmers compared to minimizers

Building from source on Linux

There is a Makefile. It will build the binary, but it does not have header file dependencies so be careful if you edit headers. You need the gcc compiler. There are no dependencies on third-party libraries. The Makefile uses ccache, if you don't have ccache installed then edit the Makefile to delete it.

Building from source on Windows

There is a Microsoft Visual Studio project file for VS 2017 (v15.4). This will probably work if imported into newer VS versions, I didn't test this.

Calculate submer metrics on a random string

syncmer -newbench output.tsv [options]

Metrics are written to output.tsv in tab-separarated text format. Options:

-k nn or -klo nn -khi nn Value(s) of k to test (k-mer length).

-s nn or -slo nn -klo nn Value(s) of s (syncmer substring length).

-w nn or -wlo nn -whi nn Values(s) of w (minimizer window length).

-d nn Integer down-sampling parameter.

-pctid nn or -pctidlo nn -pctidhi nn -pctidinc nn Mutation rate(s).

-seqlength nn Random sequence length. Default 1000000.

-pcitidout pctid.tsv Writes pctid metrics to tabbed file.

spacingout spacing.tsv Writes spacing frequencies to tabbed file.

If the lo & hi variants of an option are specified, then all values from lo to hi are tested.

Examples

syncmer -newbench results.tsv -k 15 -m 10 -pctidlo 75 -pctidhi 95 -pcitidinc 5

syncmer -newbench results.tsv -k 15 -slo 2 -shi 13 -pctidlo 80 -pctidhi 90 -pcitidinc 10

Whole-genome alignment

sycnmer -searchsix genome1.fasta -db genome2.fasta -sts ST -k K -w W -t T -log results.txt

ST is the submer type: Minimizer1 for minimizers or Syncmer5 for syncmers. K is the kmer length, W is the minimizer window length, T is the syncmer substring length (same as -s parameter for -newbench command).

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
.gitignore		.gitignore
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
alpha.cpp		alpha.cpp
alpha.h		alpha.h
alpha2.cpp		alpha2.cpp
bench.cpp		bench.cpp
bench1.cpp		bench1.cpp
bench2.cpp		bench2.cpp
bestmatch1.h		bestmatch1.h
cigar.cpp		cigar.cpp
cigar.h		cigar.h
cmds.h		cmds.h
compress.cpp		compress.cpp
countsort.h		countsort.h
cov1fract.cpp		cov1fract.cpp
depthdist.cpp		depthdist.cpp
dict.cpp		dict.cpp
equiv.cpp		equiv.cpp
fastaseqsource.cpp		fastaseqsource.cpp
fastaseqsource.h		fastaseqsource.h
fastq.cpp		fastq.cpp
fastq.h		fastq.h
fastqseqsource.cpp		fastqseqsource.cpp
fastqseqsource.h		fastqseqsource.h
fileseqsource.cpp		fileseqsource.cpp
fileseqsource.h		fileseqsource.h
filetype.cpp		filetype.cpp
filetype.h		filetype.h
gobuff.h		gobuff.h
hashtable.cpp		hashtable.cpp
jenkinshash.h		jenkinshash.h
kmer.cpp		kmer.cpp
kmer.h		kmer.h
linereader.cpp		linereader.cpp
linereader.h		linereader.h
lockobj.cpp		lockobj.cpp
lockobj.h		lockobj.h
lockobjs.h		lockobjs.h
makespindex.cpp		makespindex.cpp
mum2breaks.cpp		mum2breaks.cpp
murmur.h		murmur.h
myopts.h		myopts.h
myutils.cpp		myutils.cpp
myutils.h		myutils.h
newbench.cpp		newbench.cpp
obj.h		obj.h
objmgr.cpp		objmgr.cpp
objmgr.h		objmgr.h
objtype.h		objtype.h
objtypes.h		objtypes.h
omplock.h		omplock.h
paf2aln.cpp		paf2aln.cpp
paf2features.cpp		paf2features.cpp
pair.cpp		pair.cpp
prime.cpp		prime.cpp
primes.h		primes.h
quarts.cpp		quarts.cpp
quarts.h		quarts.h
randseq.cpp		randseq.cpp
randseq.h		randseq.h
searchsix.cpp		searchsix.cpp
searchsix.h		searchsix.h
seqdb.cpp		seqdb.cpp
seqdb.h		seqdb.h
seqdbfromfasta.cpp		seqdbfromfasta.cpp
seqinfo.cpp		seqinfo.cpp
seqinfo.h		seqinfo.h
seqsource.cpp		seqsource.cpp
seqsource.h		seqsource.h
sort.h		sort.h
spacing.cpp		spacing.cpp
spacings.cpp		spacings.cpp
speciesalign.cpp		speciesalign.cpp
speciesindex.cpp		speciesindex.cpp
speciesindex.h		speciesindex.h
speciessearch.cpp		speciessearch.cpp
spindex.cpp		spindex.cpp
spindex.h		spindex.h
stypes.h		stypes.h
syncmer.sln		syncmer.sln
syncmer.vcxproj		syncmer.vcxproj
syncmer.vcxproj.filters		syncmer.vcxproj.filters
syncmer.vcxproj.user		syncmer.vcxproj.user
syncmer_main.cpp		syncmer_main.cpp
syncmerindex.cpp		syncmerindex.cpp
syncmerindex.h		syncmerindex.h
syncmerindex2.cpp		syncmerindex2.cpp
syncmerindex2.h		syncmerindex2.h
test.cpp		test.cpp
testdist.cpp		testdist.cpp
testminimizers.cpp		testminimizers.cpp
testsubmers.cpp		testsubmers.cpp
ver.h		ver.h
wga.cpp		wga.cpp

License

rcedgar/syncmer

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