cd into the root directory (containing the 'Makefile') and type:
make
./readspam [options] <filelist>
The program takes a plain text file containing the relative paths to each input dataset. To create your 'filelist' simply type:
ls -1 path/to/input/* > filelist
This will list each file in specified directory, one file per line.
-h: print this help and exit
-k <integer>: pattern weight (default 12)
-l <integer>: don't care positions (default 100)
-t <integer>: numer of threads (default: 10)
-s <integer>: the minimum score of a spaced-word match to be considered homologous (default: 0)
Sequence must be in FASTA format. All protein sequences of one proteome must be contained in one FASTA file.
Example:
>Read1
ATAGTAGATGAT..
>Read2
ATAGTAGATGAT..
>Read3
ATGATGATGATGATG..
..
Scientific publications using Read-SpaM should cite:
A.K. Lau, C.-A. Leimeister, B. Morgenstern (2019)
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
bioRxiv, doi:10.1101/550632
https://www.biorxiv.org/content/10.1101/550632v1
In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for
example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics. Herein, we adapt our previously
developed software program Filtered Spaced-Word Matches (FSWM) for alignment-free phylogeny reconstruction to work on unassembled reads; we call this implementation
Read-SpaM. Test runs on simulated reads from bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary
distances and for very low sequencing coverage.
bmorgen (at) gwdg.de