SELDLA (Scaffold Extender with Low Depth Linkage Analysis) is the tool for generating linkage maps and draft genomes with low depth (<1x) sequencing data. SELDLA is written by C# with .NET Core, and it is executable on Windows (7-), Mac (10.12-) and Linux (Ubuntu 14.04-, CentOS 6-).
Download the zip file from here and unzip. Then, open PowerShell or Command prompt, and run SELDLA.exe.
Install .NET Core Runtime.
https://www.microsoft.com/net/download
In summary (in CentOS7),
sudo rpm -Uvh https://packages.microsoft.com/config/rhel/7/packages-microsoft-prod.rpm
sudo yum update
sudo yum install aspnetcore-runtime-2.2
sudo yum install libgdiplus-devel
Then, download SELDLA binary from here and unzip.
unzip SELDLA_x.x.x.zip
Then, run SELDLA binary.
SELDLA_v2.x.x/linux-x64/SELDLA
-
FASTA file (to be extended)
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VCF file (SNV information on the above FASTA file)
-
family file (tell father and mother ID, tab separated)
In crossbreed mode, the first column indicates the half parent's ID of which genome you want to extend, and the second column is another parent's ID in the VCF file. The columns after the third column indicate children's IDs.
In haploid mode, first column indicates a parent's ID in the VCF file, and the columns after the second column indicate children's IDs.
In duploid mode (such as RAD-seq), 1 family needs to be written in 2 rows. The first and the second columns of the first row indicate father's and mother's IDs, and the first and the second columns of the second row indicates mother's and father's IDs.
Example files can be downloaded here.
Recommended options to try first
- For crossbreed mode
SELDLA_v2.x.x/linux-x64/SELDLA --vcf=male.vcf --fasta=fourth_assembly.fasta --family=family.txt --mode=crossbreed
- For duploid mode assuming RAD-seq etc.
SELDLA_v2.x.x/linux-x64/SELDLA --vcf=input.vcf --fasta=assembly.fasta --family=family.txt --mode=duploid --DP=5 --GQ=20 -r 100 --cs=3 --MaxLdClusterOnly --noNewVcf
You will get the extended FASTA file, the lift overed vcf file and the linkage map like bellow.
The options are listed below.
--DP=VALUE DP_threshold at the cleanupVcf step [1]
--GQ=VALUE GQ_threshold at the cleanupVcf step [0]
--NonZeroSampleRate=VALUE
exclude ambiquous SNP at the cleanupVcf step (0-1) [0.3]
-p, --hqsnp=VALUE high quality SNP rate at the splitVcf step [0.3]
-b, --bal=VALUE 0 / 1 balance at the splitVcf step [0.1]
--NeedSort If the input vcf file is not sorted, use this option at the splitVcf step
--nl=VALUE near SNP match rate at the Snp2Ld step (0.5-1) [0.9]
-r=VALUE the region to merge near SNP at the Snp2Ld step (bp) [10000]
--RateOfNotNASNP=VALUE threshold of the ratio that is not NA with each other when comparing SNP at the Snp2Ld step [0.2]
-l, --clmatch=VALUE cluster match rate at the Ld2Ph step [0.8]
--cs=VALUE cluster size at the Ld2Ph step [2]
-v, --spmatch=VALUE split match rate at the Ld2Ph step to break mis-assembled contigs (0.5-1) [0.7]
--ldnum=VALUE the minimum number of same LD at the Ld2Ph step [1]
--ldseqnum=VALUE the minimum number of consecutive LDs at the Ld2Ph step [1]
--UseAllLDClusters use all LD clusters at the Ld2Ph step
--RateOfNotNALD=VALUE threshold of the ratio that is not NA with each other when comparing LD at the LD2Ph step [0.4]
--RemoveLowQualityPhases=VALUE
remove low quality phases after the LD2Ph step (yes/no) [no]
-s, --exmatch=VALUE extension match rate at the Chain step (0.5-1) [0.7]
--NonZeroPhaseRate=VALUE
exclude ambiquous Phase at the Chain step (0-1) [0.3]
--noNewVcf no converted vcf output with new position
-o, --output=VALUE output prefix [seldla]
--vcf=VALUE input VCF file <required>
--fasta=VALUE input FASTA file <required>
--family=VALUE input family file <required>
--precleaned=VALUE pre-calculated cleaned vcf file (if this option is used, input vcf is not used.)
--mode=VALUE analysis mode (crossbreed, haploid, duploid, selfpollination) [crossbreed]
-h, --help show help.
The parameter that has the biggest impact is --exmatch, which when lowered to 0.5, all contigs are connected to one. The default value is 0.7, but you can try lowering it to 0.65 or so. The threshold for splitting a misassembled contig is the option of --spmatch, this disconnects the contig in phases with a match rate below the threshold. If this value is set to 0.5, no contigs will be disconnected. The recommended value is between 0.5 and the value of --exmatch.
- Overview of SELDLA principles
