Parameters used to assemble Taphrina betulina UCD315

Skewer v0.2.2
skewer -m pe -q 15 -n

SPADES v3.11.1
spades.py --careful

Augustus v2.5.5
augustus --gff3=on --species=schizosaccharomyces_pombe

tRNAscan-SE version 2.0.3.
tRNAscan-SE -M mtDNA.fasta 
tRNAscan-SE nucleus.fasta 
(mtDNA.fasta is the mitochondrial genome scaffold, and nucleus.fasta is the whole genome assembly, excluding the mitochondrial genome scaffold)

Pipeline for variant analysis using SAMtools v1.1.19, BWA mem v0.7.12-r1039, PicardTools and Genome Analysis Toolkit v4.0.1. (including file names)

bwa index ASSEMBLY.fasta
samtools faidx ASSEMBLY.fasta
picard-tools CreateSequenceDictionary REFERENCE=ASSEMBLY.fasta OUTPUT=ASSEMBLY.dict
bwa mem -M -Y -R "@RG\tID:RGID\tSM:SAMPLE_NAME\tPL:illumina\tLB:lib1\tPU:unit1" ASSEMBLY.fasta READS1.fastq READS2.fastq > OUTPUT.sam
samtools view -S -b SAMPLE.sam > SAMPLE.bam
samtools sort SAMPLE.bam -o SAMPLE.sorted
samtools index SAMPLE.sorted
samtools flagstat SAMPLE.sorted > SAMPLE.sorted.stats
picard-tools MarkDuplicates INPUT=SAMPLE.sorted OUTPUT=SAMPLE_dedup.bam METRICS_FILE=SAMPLE_duplicates_metrics.txt VALIDATION_STRINGENCY=LENIENT
picard-tools BuildBamIndex INPUT=SAMPLE_dedup.bam VALIDATION_STRINGENCY=LENIENT
gatk HaplotypeCaller --reference ASSEMBLY.fasta --input SAMPLE_dedup.bam --output SAMPLE.vcf
bcftools stats SAMPLE.vcf > SAMPLE.vcf.stats