BOL

Third party executable parameters and options.

 

Trimmomatic

 

“ILLUMINACLIP:...:2:30:10”

“LEADING:15”

“TRAILING:15”

“SLIDINGWINDOW:4:20”

“MINLEN:20”

“TOPHRED33”

 

Filtlong

--min_length 500

--min_mean_q 85

--min_window_q 65

 

FastQ Screen

--aligner bowtie2' (bwa for PacBio)

--subset 1000 (for PacBio)

 

SPAdes

--careful

--disable-gzip-output

--cov-cutoff auto

--phred-offset 33

 

HGAP

Pbalign.task_options.min_accuracy: 70

Pbalign.task_options.no_split_subreads: false

Genomic_consensus.task_options.min_confidence: 40

falcon_ns.task_options.HGAP_GenomeLength_str:

6000000

Pbcoretools.task_options.read_length: 0

Genomic_consensus.task_options.use_score: 0

Pbalign.task_options.min_length: 50

Pbalign.task_options.algorithm_options: --minMatch 12

--bestn 10 --minPctSimilarity 70.0

Pbalign.task_options.hit_policy: randombest

Pbcoretools.task_options.other_filters: rq >= 0.7

Pbalign.task_options.concordant: false

Genomic_consensus.task_options.min_coverage: 5

falcon_ns.task_options.HGAP_SeedCoverage_str: 30

falcon_ns.task_options.HGAP_AggressiveAsm_bool: false

Genomic_consensus.task_options.algorithm: best

falcon_ns.task_options.HGAP_SeedLengthCutoff_str: -1

Genomic_consensus.task_options.diploid: false

 

MeDuSa

-random 100

 

Prokka

--usegenus

--force

--addgenes

--rfam

--rawproduct

 

cmsearch (taxonomy, 16S)

--rfam

--noali

 

blastn (taxonomy, 16S)

-evalue 1E-10

 

blastn (MLST)

-ungapped

-dust no

-evalue 1E-20

-word_size 32

-culling_limit 2

-perc_identity 95

 

blastp (VF)

-culling_limit 2

 

RGI (ABR)

--input_type contig

 

bowtie2 (mapping)

--sensitive

 

minimap2 (mapping)

-a

-x map-ont

 

samtools mpileup (SNP detection)

-uRI

 

bcftools call (SNP detection)

--variants-only

--skip-variants indels

--output-type v

--ploidy 1

-c

 

SNPsift filter (SNP detection)

"( QUAL >= 30 ) & (( na FILTER ) | (FILTER = 'PASS')) &

( DP >= 20 ) & ( MQ >= 20 )"

 

SNPeff ann (SNP detection)

-nodownload

-no-intron

-no-downstream

-no SPLICE_SITE_REGION

-upDownStreamLen 250

 

bcftools consensus

(phylogenetic tree)

--haplotype 1

 

fasttreemp

-nt

-boot 100

 

roary

-e

-n

-cd 100

-g 100000