Snapper v1.8.0
For a better rendering and navigation of this document, please download and open ./docs/snapper.docs.html, or visit https://slimsuite.github.io/snapper/.
Documentation can also be generated by running Snapper with the dochtml=T option. (R and pandoc must be installed - see below.)
Snapper is designed to generate a table of SNPs from a BLAST comparison of two genomes, map those SNPs onto genome features, predict effects and generate a series of output tables to aid exploration of genomic differences.
A basic overview of the Snapper workflow is as follows:
-
Read/parse input sequences and reference features.
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All-by-all BLAST of query "Alt" genome against reference using GABLAM.
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Reduction of BLAST hits to Unique BLAST hits in which each region of a genome is mapped onto only a single region of the other genome. This is not bidirectional at this stage, so multiple unique regions of one genome may map onto the same region of the other.
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Determine Copy Number Variation (CNV) for each region of the genome based on the unique BLAST hits. This is determined at the nucleotide level as the number of times that nucleotide maps to unique regions in the other genome, thus establishing the copy number of that nucleotide in the other genome.
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Generate SNP Tables based on the unique local BLAST hits. Each mismatch or indel in a local BLAST alignment is recorded as a SNP.
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Mapping of SNPs onto reference features based on SNP reference locus and position.
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SNP Type Classification based on the type of SNP (insertion/deletion/substitution) and the feature in which it falls. CDS SNPs are further classified according to codon changes.
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SNP Effect Classification for CDS features predicting their effects (in isolation) on the protein product.
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SNP Summary Tables for the whole genome vs genome comparison. This includes a table of CDS Ratings based on the numbers and types of SNPs. For the
*.summary.tdtoutput is, each SNP is only mapped to a single feature according to the FTBest hierarchy, removing SNPs mapping to one feature type from feature types lower in the list:
- CDS,mRNA,tRNA,rRNA,ncRNA,misc_RNA,gene,mobile_element,LTR,rep_origin,telomere,centromere,misc_feature,intergenic
Version 1.1.0 introduced additional fasta output of the genome regions with zero coverage in the other genome, i.e.
the regions in the *.cnv.tdt file with CNV=0. Regions smaller than nocopylen=X [default=100] are deleted and then
those within nocopymerge=X [default=20] of each other will be merged for output. This can be switched off with
nocopyfas=F.
Version 1.6.0 added filterself=T/F to filter out self-hits prior to Snapper pipeline. seqin=FILE sequences that are
found in the Reference (matched by name) will be renamed with the prefix alt and output to *.alt.fasta. This is
designed for identifying unique and best-matching homologous contigs from whole genome assemblies, where seqin=FILE
and reference=FILE are the same. In this case, it is recommended to increase the localmin=X cutoff.
Version 1.7.0 add the option to use minimap2 instead of BLAST+ for speed, using mapper=minimap.
Snapper is written in Python 2.x and can be run directly from the commandline:
python $CODEPATH/snapper.py [OPTIONS]
If running as part of SLiMSuite, $CODEPATH will be the SLiMSuite tools/
directory. If running from the standalone Snapper git repo, $CODEPATH
will be the path the to code/ directory. Please see details in the Snapper git repo
for running on example data.
Either blast+ or minimap2 must be installed and either added to the
environment $PATH or given to Snapper with the blast+path or minimap2=PROG settings.
To generate documentation with dochtml, R will need to be installed and a pandoc environment variable must be set, e.g.
export RSTUDIO_PANDOC=/Applications/RStudio.app/Contents/MacOS/pandoc
For Snapper documentation, run with dochtml=T and read the *.docs.html file generated.
A list of commandline options can be generated at run-time using the -h or help flags. Please see the general
SLiMSuite documentation for details of how to
use commandline options, including setting default values with INI files.
### ~ Input/Output options ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
seqin=FASFILE : Input genome to identify variants in []
reference=FILE : Fasta (with accession numbers matching Locus IDs) or genbank file of reference genome. []
basefile=FILE : Root of output file names (same as SNP input file by default) [<SNPFILE> or <SEQIN>.vs.<REFERENCE>]
nocopyfas=T/F : Whether to output CNV=0 fragments to *.nocopy.fas fasta file [True]
nocopylen=X : Minimum length for CNV=0 fragments to be output [100]
nocopymerge=X : CNV=0 fragments within X nt of each other will be merged prior to output [20]
makesnp=T/F : Whether or not to generate Query vs Reference SNP tables [True]
localsAM=T/F : Save local (and unique) hits data as SAM files in addition to TDT [False]
filterself=T/F : Filter out self-hits prior to Snapper pipeline (e.g for assembly all-by-all) [False]
mapper=X : Program to use for mapping files against each other (blast/minimap) [blast]
dochtml=T/F : Generate HTML Snapper documentation (*.docs.html) instead of main run [False]
### ~ Reference Feature Options ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
spcode=X : Overwrite species read from file (if any!) with X if generating sequence file from genbank [None]
ftfile=FILE : Input feature file (locus,feature,position,start,end) [*.Feature.tdt]
ftskip=LIST : List of feature types to exclude from analysis [source]
ftbest=LIST : List of features to exclude if earlier feature in list overlaps position [(see above)]
### ~ SNP Mapping Options ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
snpmap=FILE : Input table of SNPs for standalone mapping and output (should have locus and pos info) [None]
snphead=LIST : List of SNP file headers []
snpdrop=LIST : List of SNP fields to drop []
altpos=T/F : Whether SNP file is a single mapping (with AltPos) (False=BCF) [True]
altft=T/F : Use AltLocus and AltPos for feature mapping (if altpos=T) [False]
localsort=X : Local hit field used to sort local alignments for localunique reduction [Identity]
localmin=X : Minimum length of local alignment to output to local stats table [10]
localidmin=PERC : Minimum local %identity of local alignment to output to local stats table [0.0]
### ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
© 2021 Richard Edwards | richard.edwards@unsw.edu.au