main-slots-tools.txt

abyss-pe
align_families
alleyoop
bg_diamond
bg_diamond_makedb
bio_hansel
bowtie2
bowtie_color_wrapper
bowtie_wrapper
busco
bwa
bwa_color_wrapper
bwa_mem
bwameth
bwa_wrapper
correct_barcodes
cuffdiff
cufflinks
cuffmerge
cuffnorm
cuffquant
cutadapt
dada2_assignTaxonomyAddspecies
dada2_dada
dada2_learnErrors
deseq2
dexseq
disco
dunovo
egsea
exonerate
fargene
fasterq_dump
fastp
featurecounts
flash
freebayes
gatk4_mutect2
gatk_count_covariates
gatk_realigner_target_creator
gatk_unified_genotyper
gatk_variant_eval
gatk_variant_recalibrator
gatk_variant_select
gubbins
heinz
hifive
hisat2
iqtree
iuc_pear
kallisto_pseudo
kallisto_quant
kobas_annotate
kraken
kraken2
lastz_wrapper_2
lofreq_call
lofreq_viterbi
maker
maxbin2
metaspades
migmap
minimap2
mlst
mothur_align_seqs
mothur_chimera_bellerophon
mothur_chimera_ccode
mothur_chimera_check
mothur_chimera_perseus
mothur_chimera_pintail
mothur_chimera_slayer
mothur_chimera_uchime
mothur_chimera_vsearch
mothur_chop_seqs
mothur_classify_seqs
mothur_cluster_split
mothur_dist_seqs
mothur_dist_shared
mothur_filter_seqs
mothur_get_communitytype
mothur_indicator
mothur_make_contigs
mothur_metastats
mothur_pairwise_seqs
mothur_parsimony
mothur_pcr_seqs
mothur_phylo_diversity
mothur_pre_cluster
mothur_primer_design
mothur_rarefaction_single
mothur_screen_seqs
mothur_seq_error
mothur_shhh_flows
mothur_shhh_seqs
mothur_summary_seqs
mothur_summary_shared
mothur_tree_shared
mothur_trim_flows
mothur_trim_seqs
mothur_unifrac_unweighted
mothur_unifrac_weighted
multigps
mummer_nucmer
nanoplot
nonpareil
pilon
pipelign
plant_tribes_assembly_post_processor
plant_tribes_gene_family_aligner
plant_tribes_gene_family_classifier
plant_tribes_gene_family_phylogeny_builder
plant_tribes_kaks_analysis
presto_alignsets
presto_assemblepairs
presto_buildconsensus
presto_filterseq
presto_maskprimers
prokka
qualimap_bamqc
quast
rbc_mafft
repeatmasker_wrapper
rnaspades
rna_star
roary
sailfish
salmon
sam_to_bam
samtools_slice_bam
samtools_sort
scpipe
seqtk_mergefa
seqtk_mergepe
shovill
sina
sklearn_build_pipeline
sklearn_ensemble
sklearn_model_validation
sklearn_numeric_clustering
slamdunk
snippy
socru
spades
spaln
star_fusion
stringtie
stringtie_merge
tag_pileup_frequency
tb_profiler_profile
td
tetyper
tophat
tophat2
tophat_fusion_post
transdecoder
trimmomatic
trinity
trinity_align_and_estimate_abundance
trinity_psc
unicycler
valet
varscan_somatic
velvetoptimiser