Table 6 Software and parameters used during the #R1 genome sequencing, assembly and annotation.
From: Chromosome-scale genome assembly and annotation of Paspalum notatum Flüggé var. saurae
Software | Parameters | Reference |
|---|---|---|
guppyGPU v6.0.6 | -c dna_r9.4.1_450bps_hac.cfg -r --num_callers 4 --gpu_runners_per_device 8 --qscore_filtering --min_qscore 7 -x cuda:3 | |
NanoPlot v1.31.0 | default | |
Flye v2.9 | --threads 32 --nano-hq --genome-size 600 m | |
Racon-gpu v1.4.10 | default | |
RagTag v2.1.0 | scaffold -C -r --aligner minimap2 --mm2-params -x asm5 | |
Bwa v0.7.17 | mem | |
Pilon v1.23 | --fix all --changes --diploid | |
Jellyfish v2.3.0 | count -C -m 21 -s 10000000000 -t 12 | histo -h 10000000 -t 10 | |
GenomeScope | kmer = 21, read length = 200, max kmer coverage = 50.000.000 | |
BUSCO v5 | ortholog set = OrthoDB v10 – Liliopsida | |
Trimmomatic v0.33 | PE -phred33 CROP:230 ILLUMINACLIP:Illumina SLIDINGWINDOW:4:30 | |
RepeatExplorer2 v4.1.2 | default | |
RepeatModeler v4.1.2 | -database R1_rep -engine rmblast | |
RepeatMasker v4.1.2 | -e rmblast -nolow -norna -pa 4 -s -html -gff -lib R1_rep-families.fa | |
stringtie v2.2.1 | -L–ref | |
Trinity v2.0.2 | --seqType fq --max_memory 30 G --CPU 4 --min_contig_length 300 --group_pairs_distance 500 --no_version_check --verbose --full_cleanup --genome_guided_bam --genome_guided_max_intron 5000 | |
NanoFilt v1.0 | -q 10 -l 5000 (DNA) -q 10 -l 300 --headcrop 85 --tailcrop 85 (cDNA) | |
BLAST + /2.13.0 | -evalue 0.00001 -perc_identity 80 -qcov_hsp_perc 80 (centromeric regions) | |
quarTeT v1.2.1 | TeloExplorer -c plant -m 5 | |
MAKER v2.31.9 | max_dna_len = 100000 min_contig = 1 pred_flank = 200 alt_splice = 1 split_hit = 10000 single_exon = 1 single_length = 250 est2genome = 1 (run 1) est2genome = 0 (run 2) | |
Exonerate v2.4.0 | integrated to MAKER pipeline | |
CD-HIT v4.8.1 | Cd-hit-est -c 0.9 -n 8 -d 0 -T 8 -M 1000 | |
AUGUSTUS v3.2.2 | integrated to MAKER pipeline: augustus_species = rice (run 1) augustus_species = custom (run2) | |
SNAP | integrated to MAKER pipeline: snap_hmmm = custom (run 2) | |
GffReadv0.12.7 | -y -x / -J (high confidence genes) | |
InterProScan v5.53.87.0 | -appl TIGRFAM,SFLD,SUPERFAMILY,PANTHER,SMART,CDD,PIRSR,Pfam,MobiDBLite -f TSV,GFF3 -goterms | |
Barnap v0.9 | --reject 0.9 --lencutoff 0.9 --evalue 1e-10 --kingdom eukA9:AMJ9 | |
tRNAscan-SE v1.3.1 | --infernal | |
ShortStack v3.8.4 | --mismatches 2 --bowtie_cores 6 | |
TargetFinder | -r -t 20 -c 4 | |
NCBI-FCS-GX | --tax-id “1”--div “plnt:plants”--split-fasta “true”--gx-db gxdb --action-report true | |
Merqury | default / meryl kmer = 21 |
