<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36514?offset=350 https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools Thu, 16 Jan 2020 23:14:00 -0600 https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools <![CDATA[ngs-bits - Short-read sequencing tools]]> Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Address of the bookmark: https://github.com/imgag/ngs-bits

]]> Neel 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 https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis Wed, 18 Aug 2021 00:02:54 -0500 https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis <![CDATA[Kmer: a suite of tools for DNA sequence analysis]]> More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

  • A2Amapper: ATAC, Assembly to Assembly Comparision tool:
    • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).
  • Sim4db:
    • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.
  • LEAFF:
    • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.
  • Meryl:
    • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation Tue, 18 Jun 2024 02:04:39 -0500 https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation <![CDATA[BioKit: a set of tools dedicated to bioinformatics, data visualisation]]> BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g., biokit.stats). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

]]> Neel