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ROSE

Augustus[optimize_augustus]

Augustus[new_species]

Augustus[randomSplit]

Augustus[join_aug_pred]

Augustus[filterGenesIn]

Augustus[getAnnoFasta]

Augustus[gtf2gff]

Augustus[prepareAlign]

Augustus[pp_simScore]

Augustus[load2sqlitedb]

Augustus[load2db]

Augustus[joingenes]

Augustus[homGeneMapping]

Augustus[getSeq]

Augustus[filterBam]

Augustus[fastBlockSearch]

Augustus[etraining]

Augustus[compileSpliceCands]

Augustus[bam2wig]

Augustus[bam2hints]

Augustus[augustus]

Augustus[aln2wig]

ANNOVAR[variants_reduction]

ANNOVAR[coding_change]

ANNOVAR[retrieve_seq_from_fasta]

ANNOVAR[table_annovar]

ANNOVAR[annotate_variation]

ANNOVAR[convert2annovar]

ZGA

Wise2

VIBRANT

VCFtools

TRUST4

Trimmomatic

TrimGalore

TPMCalculator

SVcnn

SvABA

SURVIVOR

subread

StringTie

Strelka2

STAR

sra-tools

SPAdes

spaceranger

somalier

SNAP

Sickle

SHAPEIT5

SemiBin

Samtools

RSEM

Roary

QualiMap

ProtHint

Prokka

Picard

MUMmer

mothur

minimap2

miniasm

Merqury

MEGAHIT

Manta

MaAsLin2

LUMPY

Kreaken2

IGV

HTSlib

HOMER

HISAT-3N

HISAT2

hifiasm

GRIDSS

graphtyper

gnuplot

gffread

GeneMark-ETP

GATK

FASTX-Toolkit

FastQC

fastp

Dsuite

DIAMOND

Delly

DAS_Tool

CoverM

CNVnator

cellranger

cd-hit

cdbfasta

Canvas

Canu

BWA

BUSCO

BRAKER

Bracken

Bowtie2

Bowtie

BLAST

blas

Bismark

bedtools

bedtools

BCFtools

bamtools

bam-readcount

Augustus

ANNOVAR

3D-DNA