snp-dists

Convert a FASTA alignment to SNP distance matrix

Quick Start

% cat test/good.aln

>seq1
AGTCAGTC
>seq2
AGGCAGTC
>seq3
AGTGAGTA
>seq4
TGTTAGAC

% snp-dists test/good.aln > distances.tab

Read 4 sequences of length 8

% cat distances.tab

snp-dists 0.7   seq1    seq2    seq3    seq4
seq1            0       1       2       3
seq2            1       0       3       4
seq3            2       3       0       4
seq4            3       4       4       0

Installation

snp-dists is written in C to the C99 standard and only depends on zlib.

Bioconda

conda install -c bioconda snp-dists

Containers

Docker images are available on dockerhub and quay.io. These are maintained by the StaPH-B workgroup. Dockerfiles can be found here.

# Docker
docker pull staphb/snp-dists:latest
docker run staphb/snp-dists:latest snp-dists -h

# Singularity
singularity build snp-dists.sif docker://staphb/snp-dists:latest
singularity exec snp-dists.sif snp-dists -h

Source

git clone https://github.com/tseemann/snp-dists.git
cd snp-dists
make

# run tests
make check
bats test/test.sh # if you have BATS installed

# install into $HOME/.local/bin
make install

Options

snp-dists -h (help)

USAGE
  snp-dists [opts] aligned.fasta[.gz] > matrix.tsv
OPTIONS
  -h       Show this help
  -v       Print version and exit
  -j CPUS  Threads to use [1]
  -q       Quiet mode; no progress messages
  -a       Count all differences not just [AGTC]
  -k       Keep case, don't uppercase all letters
  -m       Output MOLTEN instead of TSV
  -L       Ootput lower-trangle only (unique pairs)
  -c       Use comma instead of tab in output
  -b       Blank top left corner cell
  -t       Add column headers when using molten format
  -x INT   Stop counting distance beyond this [99999]
URL
  https://github.com/tseemann/snp-dists

snp-dists -v (version)

Prints the name and version separated by a space in standard Unix fashion.

snp-dists 0.9.0

snp-dists -q (quiet mode)

Don’t print informational messages, only errors.

snp-dists -c (CSV instead of TSV)

snp-dists 0.7.0,seq1,seq2,seq3,seq4
seq1,0,1,2,3
seq2,1,0,3,4
seq3,2,3,0,4
seq4,3,4,4,0

snp-dists -b (omit the toolname/version)

        seq1    seq2    seq3    seq4
seq1    0       1       2       3
seq2    1       0       3       4
seq3    2       3       0       4
seq4    3       4       4       0

snp-dists -L (lower-triangle only)

    seq1    seq2    seq3    seq4
seq1    0
seq2    1    0
seq3    2    3    0
seq4    3    4    4    0

Advanced options

By default, all letters are (1) uppercased and (2) ignored if not A,G,T or C.

snp-dists -a (don’t just count AGTC)

Normally one would not want to count ambiguous letters and gaps as a “difference” but if you desire, you can enable this option.

>seq1
NGTCAGTC
>seq2
AG-CAGTC
>seq3
AGTGNGTA

snp-dists -k (don’t uppercase any letters)

You may wish to preserve case, as you may wish lower-case characters to be masked in the comparison.

>seq1
AgTCAgTC
>seq2
AggCAgTC
>seq3
AgTgAgTA

snp-dists -m (“molten” output format)

seq1    seq1    0
seq1    seq2    1
seq1    seq3    2
seq1    seq4    3
seq2    seq1    1
seq2    seq2    0
seq2    seq3    3
seq2    seq4    4
seq3    seq1    2
seq3    seq2    3
seq3    seq3    0
seq3    seq4    4
seq4    seq1    3
seq4    seq2    4
seq4    seq3    4
seq4    seq4    0

snp-dists -m -t (“molten” output format with column headers; requires -m “molten” format enabled)

sequence_1  sequence_2  distance
seq1        seq1        0
seq1        seq2        1
seq1        seq3        2
<snip>

snp-dists -x INT (stop counting after INT SNPs

Once a distance between two samples becomes very large there is often not much point keeping on counting. Th -x option allows you to “short-circuit” the counting. This can reduce computation time significantly on large alignment is you only care about small distance.

Issues

Report bugs and give suggesions on the Issues page

Related software

• pairsnp
• Disty
• Panito
• pairwise_snp_differences

Licence

GPL Version 3

Authors

• Torsten Seemann
• Fabian Klötzl
• Andrew J Page