<![CDATA[BOL: Frequent parameters for bioinformatics tools !]]> https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools? https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools Tue, 27 Oct 2020 19:42:32 -0500 https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools <![CDATA[Frequent parameters for bioinformatics tools !]]>
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
]]> BioStar