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A versatile toolkit for k-mers with taxonomic information

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shenwei356/unikmer

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Documents:https://bioinf.shenwei.me/unikmer/

unikmer is a toolkit for nucleic acidk-mer analysis,providing functionsincluding set operation k-mers (sketch) optional withTaxIds but without count information.

K-mers are either encoded (k<=32) or hashed (k<=64, using ntHash v1) intouint64,and serialized in binary file with extension.unik.

TaxIds can be assigned when counting k-mers from genome sequences,and LCA (Lowest Common Ancestor) is computed during set opertionsincluding computing union, intersecton, set difference, unique andrepeated k-mers.

Related projects:

Table of Contents

Using cases

  • Finding conserved regions in all genomes of a species.
  • Finding species/strain-specific sequences for designing probes/primers.

Installation

  1. Downloadingexecutable binary files.

  2. Via BiocondaAnaconda Clouddownloads

     conda install -c bioconda unikmer

Commands

Usages

  1. Counting

     count           Generate k-mers (sketch) from FASTA/Q sequences

  2. Information

     info            Information of binary files num             Quickly inspect the number of k-mers in binary files

  3. Format conversion

     view            Read and output binary format to plain text dump            Convert plain k-mer text to binary format encode          Encode plain k-mer texts to integers decode          Decode encoded integers to k-mer texts

  4. Set operations

     concat          Concatenate multiple binary files without removing duplicates inter           Intersection of k-mers in multiple binary files common          Find k-mers shared by most of the binary files union           Union of k-mers in multiple binary files diff            Set difference of k-mers in multiple binary files

  5. Split and merge

     sort            Sort k-mers to reduce the file size and accelerate downstream analysis split           Split k-mers into sorted chunk files tsplit          Split k-mers according to TaxId merge           Merge k-mers from sorted chunk files

  6. Subset

     head            Extract the first N k-mers sample          Sample k-mers from binary files grep            Search k-mers from binary files filter          Filter out low-complexity k-mers rfilter         Filter k-mers by taxonomic rank

  7. Searching on genomes

     locate          Locate k-mers in genome map             Mapping k-mers back to the genome and extract successive regions/subsequences

  8. Misc

     autocompletion  Generate shell autocompletion script version         Print version information and check for update

Binary file

Go Reference

K-mers (represented inuint64 in RAM ) are serialized in 8-Byte(or less Bytes for shorter k-mers in compact format,or much less Bytes for sorted k-mers) arrays andoptionally compressed in gzip format with extension of.unik.TaxIds are optionally stored next to k-mers with 4 or less bytes.

Compression ratio comparison

No TaxIds stored in this test.

cr.jpg

labelencoded-kmeragzip-compressedbcompact-formatcsorteddcomment
plainplain text
gzip✔gzipped plain text
unik.default✔✔gzipped encoded k-mers in fixed-length byte array
unik.compat✔✔✔gzipped encoded k-mers in shorter fixed-length byte array
unik.sorted✔✔✔gzipped sorted encoded k-mers
  • a One k-mer is encoded asuint64 and serialized in 8 Bytes.
  • b K-mers file is compressed in gzip format by default,users can switch on global option-C/--no-compress to output non-compressed file.
  • c One k-mer is encoded asuint64 and serialized in 8 Bytes by default.However few Bytes are needed for short k-mers, e.g., 4 Bytes are enough for15-mers (30 bits). This makes the file more compact with smaller file size,controled by global option-c/--compact.
  • d One k-mer is encoded asuint64, all k-mers are sorted and compressedusing varint-GB algorithm.
  • In all test, flag--canonical is ON when runningunikmer count.

Quick Start

# memusg is for compute time and RAM usage: https://github.com/shenwei356/memusg# counting (only keep the canonical k-mers and compact output)# memusg -t unikmer count -k 23 Ecoli-IAI39.fasta.gz -o Ecoli-IAI39.fasta.gz.k23 --canonical --compact$ memusg -t unikmer count -k 23 Ecoli-MG1655.fasta.gz -o Ecoli-MG1655.fasta.gz.k23 --canonical --compactelapsed time: 0.897speak rss: 192.41 MB# counting (only keep the canonical k-mers and sort k-mers)# memusg -t unikmer count -k 23 Ecoli-IAI39.fasta.gz -o Ecoli-IAI39.fasta.gz.k23.sorted --canonical --sort$ memusg -t unikmer count -k 23 Ecoli-MG1655.fasta.gz -o Ecoli-MG1655.fasta.gz.k23.sorted --canonical --sortelapsed time: 1.136speak rss: 227.28 MB# counting and assigning global TaxIds$ unikmer count -k 23 -K -s Ecoli-IAI39.fasta.gz -o Ecoli-IAI39.fasta.gz.k23.sorted   -t 585057$ unikmer count -k 23 -K -s Ecoli-MG1655.fasta.gz -o Ecoli-MG1655.fasta.gz.k23.sorted -t 511145$ unikmer count -k 23 -K -s A.muciniphila-ATCC_BAA-835.fasta.gz -o A.muciniphila-ATCC_BAA-835.fasta.gz.sorted -t 349741# counting minimizer and ouputting in linear order$ unikmer count -k 23 -W 5 -H -K -l A.muciniphila-ATCC_BAA-835.fasta.gz -o A.muciniphila-ATCC_BAA-835.fasta.gz.m# view$ unikmer view Ecoli-MG1655.fasta.gz.k23.sorted.unik --show-taxid | head -n 3AAAAAAAAACCATCCAAATCTGG 511145AAAAAAAAACCGCTAGTATATTC 511145AAAAAAAAACCTGAAAAAAACGG 511145# view (hashed k-mers needs original FASTA/Q file)$ unikmer view --show-code --genome A.muciniphila-ATCC_BAA-835.fasta.gz A.muciniphila-ATCC_BAA-835.fasta.gz.m.unik | head -n 3CATCCGCCATCTTTGGGGTGTCG 1210726578792AGCGCAAAATCCCCAAACATGTA 2286899379883AACTGATTTTTGATGATGACTCC 3542156397282# find the positions of k-mers$ unikmer locate -g A.muciniphila-ATCC_BAA-835.fasta.gz A.muciniphila-ATCC_BAA-835.fasta.gz.m.unik | head -n 5NC_010655.1     2       25      ATCTTATAAAATAACCACATAAC 0       .NC_010655.1     5       28      TTATAAAATAACCACATAACTTA 0       .NC_010655.1     6       29      TATAAAATAACCACATAACTTAA 0       .NC_010655.1     9       32      AAAATAACCACATAACTTAAAAA 0       .NC_010655.1     13      36      TAACCACATAACTTAAAAAGAAT 0       .# info$ unikmer info *.unik -a -j 10file                                              k  canonical  hashed  scaled  include-taxid  global-taxid  sorted  compact  gzipped  version     number  descriptionA.muciniphila-ATCC_BAA-835.fasta.gz.m.unik       23  ✓          ✓       ✕       ✕                            ✕       ✕        ✓        v5.0       860,900             A.muciniphila-ATCC_BAA-835.fasta.gz.sorted.unik  23  ✓          ✕       ✕       ✕                    349741  ✓       ✕        ✓        v5.0     2,630,905             Ecoli-IAI39.fasta.gz.k23.sorted.unik             23  ✓          ✕       ✕       ✕                    585057  ✓       ✕        ✓        v5.0     4,902,266             Ecoli-IAI39.fasta.gz.k23.unik                    23  ✓          ✕       ✕       ✕                            ✕       ✓        ✓        v5.0     4,902,266             Ecoli-MG1655.fasta.gz.k23.sorted.unik            23  ✓          ✕       ✕       ✕                    511145  ✓       ✕        ✓        v5.0     4,546,632             Ecoli-MG1655.fasta.gz.k23.unik                   23  ✓          ✕       ✕       ✕                            ✕       ✓        ✓        v5.0     4,546,632             # concat$ memusg -t unikmer concat *.k23.sorted.unik -o concat.k23 -celapsed time: 1.020speak rss: 25.86 MB# union$ memusg -t unikmer union *.k23.sorted.unik -o union.k23 -selapsed time: 3.991speak rss: 590.92 MB# or sorting with limited memory.# note that taxonomy database need some memory.$ memusg -t unikmer sort *.k23.sorted.unik -o union2.k23 -u -m 1Melapsed time: 3.538speak rss: 324.2 MB$ unikmer view -t union.k23.unik | md5sum 4c038832209278840d4d75944b29219c  -$ unikmer view -t union2.k23.unik | md5sum 4c038832209278840d4d75944b29219c  -# duplicate k-mers# memusg -t unikmer sort *.k23.sorted.unik -o dup.k23 -d -m 1M # limit memory usage$ memusg -t unikmer sort *.k23.sorted.unik -o dup.k23 -delapsed time: 1.143speak rss: 240.18 MB# intersection$ memusg -t unikmer inter *.k23.sorted.unik -o inter.k23elapsed time: 1.481speak rss: 399.94 MB# difference$ memusg -t unikmer diff -j 10 *.k23.sorted.unik -o diff.k23 -selapsed time: 0.793speak rss: 338.06 MB$ ls -lh *.unik-rw-r--r-- 1 shenwei shenwei 6.6M Sep  9 17:24 A.muciniphila-ATCC_BAA-835.fasta.gz.m.unik-rw-r--r-- 1 shenwei shenwei 9.5M Sep  9 17:24 A.muciniphila-ATCC_BAA-835.fasta.gz.sorted.unik-rw-r--r-- 1 shenwei shenwei  46M Sep  9 17:25 concat.k23.unik-rw-r--r-- 1 shenwei shenwei 9.2M Sep  9 17:27 diff.k23.unik-rw-r--r-- 1 shenwei shenwei  11M Sep  9 17:26 dup.k23.unik-rw-r--r-- 1 shenwei shenwei  18M Sep  9 17:23 Ecoli-IAI39.fasta.gz.k23.sorted.unik-rw-r--r-- 1 shenwei shenwei  29M Sep  9 17:24 Ecoli-IAI39.fasta.gz.k23.unik-rw-r--r-- 1 shenwei shenwei  17M Sep  9 17:23 Ecoli-MG1655.fasta.gz.k23.sorted.unik-rw-r--r-- 1 shenwei shenwei  27M Sep  9 17:25 Ecoli-MG1655.fasta.gz.k23.unik-rw-r--r-- 1 shenwei shenwei  11M Sep  9 17:27 inter.k23.unik-rw-r--r-- 1 shenwei shenwei  26M Sep  9 17:26 union2.k23.unik-rw-r--r-- 1 shenwei shenwei  26M Sep  9 17:25 union.k23.unik$ unikmer stats *.unik -a -j 10file                                              k  canonical  hashed  scaled  include-taxid  global-taxid  sorted  compact  gzipped  version     number  descriptionA.muciniphila-ATCC_BAA-835.fasta.gz.m.unik       23  ✓          ✓       ✕       ✕                            ✕       ✕        ✓        v5.0       860,900             A.muciniphila-ATCC_BAA-835.fasta.gz.sorted.unik  23  ✓          ✕       ✕       ✕                    349741  ✓       ✕        ✓        v5.0     2,630,905             concat.k23.unik                                  23  ✓          ✕       ✕       ✓                            ✕       ✓        ✓        v5.0            -1             diff.k23.unik                                    23  ✓          ✕       ✕       ✓                            ✓       ✕        ✓        v5.0     2,326,096             dup.k23.unik                                     23  ✓          ✕       ✕       ✓                            ✓       ✕        ✓        v5.0     2,576,170             Ecoli-IAI39.fasta.gz.k23.sorted.unik             23  ✓          ✕       ✕       ✕                    585057  ✓       ✕        ✓        v5.0     4,902,266             Ecoli-IAI39.fasta.gz.k23.unik                    23  ✓          ✕       ✕       ✕                            ✕       ✓        ✓        v5.0     4,902,266             Ecoli-MG1655.fasta.gz.k23.sorted.unik            23  ✓          ✕       ✕       ✕                    511145  ✓       ✕        ✓        v5.0     4,546,632             Ecoli-MG1655.fasta.gz.k23.unik                   23  ✓          ✕       ✕       ✕                            ✕       ✓        ✓        v5.0     4,546,632             inter.k23.unik                                   23  ✓          ✕       ✕       ✓                            ✓       ✕        ✓        v5.0     2,576,170             union2.k23.unik                                  23  ✓          ✕       ✕       ✓                            ✓       ✕        ✓        v5.0     6,872,728             union.k23.unik                                   23  ✓          ✕       ✕       ✓                            ✓       ✕        ✓        v5.0     6,872,728# -----------------------------------------------------------------------------------------# mapping k-mers to genomeseqkit seq Ecoli-IAI39.fasta.gz -o Ecoli-IAI39.fastag=Ecoli-IAI39.fastaf=inter.k23.unik# mapping k-mers back to the genome and extract successive regions/subsequencesunikmer map -g $g $f -a | more# using bwa# to fastaunikmer view $f -a -o $f.fa.gz# make indexbwa index $g; samtools faidx $gncpu=12ls $f.fa.gz \    | rush -j 1 -v ref=$g -v j=$ncpu \        'bwa aln -o 0 -l 17 -k 0 -t {j} {ref} {} \            | bwa samse {ref} - {} \            | samtools view -bS > {}.bam; \         samtools sort -T {}.tmp -@ {j} {}.bam -o {}.sorted.bam; \         samtools index {}.sorted.bam; \         samtools flagstat {}.sorted.bam > {}.sorted.bam.flagstat; \         /bin/rm {}.bam '

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A versatile toolkit for k-mers with taxonomic information

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