Examples : samtools, bed, topic:conversion

289 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset Editing 2
Add line to file writes a line of text at the begining or end of a text file. 1
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
Annotate a VCF dataset with custom filters 1
Augustus gene prediction for prokaryotic and eukaryotic genomes 8
Aurora Galaxy WGCNA Identify gene co-expression network modules using WGCNA. 1
aurora_deseq2 Differential analysis of count data with the DESeq2 package 1
aurora_dustmasker Low complexity region masker based on Symmetric DUST algorithm 1
aurora_fasta_importer Import fasta to galaxy by copying uploaded fasta or downloading fasta from an URL. 1
aurora_fastqc Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads files. 1
aurora_fastqc_site Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads files. 1
aurora_find_ssrs Identifies simple sequence repeats (SSRs) and calls primers from the sequences in a fastq formatted file. 1
aurora_freebayes Bayesian haplotype-based genetic polymorphism discovery and genotyping. 1
aurora_skewer A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads. 1
aurora_statonlab_hmmscan_merger Merge results from the aurora_statonlab_hmmscan tool and group differentially expressed genes across multiple organims by pfam 1
aurora_tool some description 1
BAM-to-SAM convert BAM to SAM 5
Bayenv Bayenv determines in local adaptation can be identified by correlation between allele frequencies and ecological variables or graphical location. 1
BayeScan2.0 BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. 1
bcf_uncompressed-to-bcf converter 1
bcftools bcftools Convert, filter, subset VCF/BCF files 1
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 14
BEAM significant single- and multi-locus SNP associations in case-control studies 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BedCov calculate read depth for a set of genomic intervals 5
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools AnnotateBed annotate coverage of features from multiple files 21
bedtools BAM to BED converter 23
bedtools BED to BAM converter 21
bedtools BED to IGV create batch script for taking IGV screenshots 16
bedtools BED12 to BED6 converter 20
bedtools BEDPE to BAM converter 21
bedtools ClosestBed find the closest, potentially non-overlapping interval 21
bedtools ClusterBed cluster overlapping/nearby intervals 20
bedtools ComplementBed Extract intervals not represented by an interval file 21
bedtools ExpandBed replicate lines based on lists of values in columns 20
bedtools FisherBed calculate Fisher statistic between two feature files 20
bedtools FlankBed create new intervals from the flanks of existing intervals 21
bedtools Genome Coverage compute the coverage over an entire genome 20
bedtools GroupByBed group by common cols and summarize other cols 20
bedtools JaccardBed calculate the distribution of relative distances between two files 20
bedtools LinksBed create a HTML page of links to UCSC locations 20
bedtools MakeWindowsBed make interval windows across a genome 21
bedtools MaskFastaBed use intervals to mask sequences from a FASTA file 20
bedtools Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 20
bedtools MergeBED combine overlapping/nearby intervals into a single interval 20
bedtools MultiCovBed counts coverage from multiple BAMs at specific intervals 20
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
bedtools OverlapBed computes the amount of overlap from two intervals 20
bedtools RandomBed generate random intervals in a genome 21
bedtools ReldistBed calculate the distribution of relative distances 20
bedtools ShuffleBed randomly redistrubute intervals in a genome 21
bedtools SlopBed adjust the size of intervals 22
bedtools SortBED order the intervals 20
bedtools SpacingBed reports the distances between features 17
bedtools SubtractBed remove intervals based on overlaps 20
bedtools TagBed tag BAM alignments based on overlaps with interval files 20
bedtools WindowBed find overlapping intervals within a window around an interval 20
Bowtie2 - map reads against reference genome 21
Change Case of selected columns 2
CleanSam perform SAM/BAM grooming 14
CML to InChI 2
CML to mol2 2
CML to SDF 2
cml-to-smi converter 2
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 14
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 14
CollectGcBiasMetrics charts the GC bias metrics 14
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 4
CollectInsertSizeMetrics plots distribution of insert sizes 14
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 15
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 14
Compare multiple VCF datasets 1
Compare two Datasets to find common or distinct rows Filtering 1
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 21
Compute quality statistics for SOLiD data 1
Condense consecutive characters 2
Convert delimiters to TAB 1
Convert SOLiD output to fastq 1
Convert delimiters 1
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Count occurrences of each record 2
Create single interval as a new dataset 1
csv-to-tabular converter 1
Data Fetch Query and retrieval 1
DAVID functional annotation for a list of genes 1
dbnsfp.tabular-to-snpsiftdbnsfp converter 3
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 22
Diamond alignment tool for short sequences against a protein database Sequence alignment analysis 9
Diamond makedb Build database from a FASTA file Sequence alignment analysis 8
Diamond view generate formatted output from DAA files Sequence alignment analysis 6
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
Draw quality score boxplot for SOLiD data 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract Pairwise MAF blocks given a set of genomic intervals 1
fasta-to-fai converter 1
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 5
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FASTQE visualize fastq files with emoji's 🧬😎 5
FastqToSam convert Fastq data into unaligned BAM 19
fastSTRUCTURE. Step 1: BED, BIM and FAM file calculation 1
fastSTRUCTURE. Step 2: Run fastSTRUCTURE 1
fastSTRUCTURE. Step 3: Create population structure file for GWAS 1
fastSTRUCTURE. Step 4: Plotting the results 1
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 25
Filter data on any column using simple expressions Formatting 2
Filter a VCF file 1
Filter GFF data by attribute using simple expressions 2
Filter GFF data by feature count using simple expressions 1
Filter GTF data by attribute values_list 2
Filter MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 6
FilterSamReads include or exclude aligned and unaligned reads and read lists 14
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
g:Profiler tools for functional profiling of gene lists 1
GATK tool collection Version 3.4-0 2
Gene BED To Exon/Intron/Codon BED expander 1
GetFastaBed use intervals to extract sequences from a FASTA file 20
GFF-to-BED converter Conversion 1
GPASS significant single-SNP associations in case-control studies 1
Group data by a column and perform aggregate operation on other columns. 4
Guppy basecaller wrapper A simple wrapper for guppy basecaller that depends on configuration files 1
GWAS with EMMAX. Step 1: SNP file from VCF to PED format 1
GWAS with EMMAX. Step 2: SNP file from PED to tPED format 1
GWAS with EMMAX. Step 3. Calculate the kinship matrix with EMMAX 1
GWAS with EMMAX. Step 4: Association mapping 1
HISAT spliced aligner 1
HISAT2 A fast and sensitive alignment program 19
IdxStats reports stats of the BAM index file 8
InChI to CML 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
inchi-to-mol converter 2
Intersect multiple VCF datasets 2
Intersect intervals find overlapping intervals in various ways 22
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
LD linkage disequilibrium and tag SNPs 1
Line/Word/Character count of a dataset 1
LinkImputeR. Step 1: Run LinkImputeR in accuracy mode 1
LinkImputeR. Step 2: Perform the final imputation 1
LPS LASSO-Patternsearch algorithm 1
MAF Coverage Stats Alignment coverage information 3
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
Map with BWA - map short reads (< 100 bp) against reference genome 12
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 14
MapBed apply a function to a column for each overlapping interval 21
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 17
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 16
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
MeanQualityByCycle chart distribution of base qualities 14
Merge multiple VCF datasets 2
Merge Columns together 4
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
MergeSamFiles merges multiple SAM/BAM datasets into one 14
Metasoft Metasoft estimates effect size, heterogeneity and M-values 1
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to SDF 2
MOL2 to SMILES 2
mol2-to-mol converter 2
mothur.ref.taxonomy-to-mothur.seq.taxonomy converter 2
Multiple Testing Correction Exploratory analysis of the population structure. 1
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 18
NormalizeFasta normalize fasta datasets 14
NucBed profile the nucleotide content of intervals in a FASTA file 21
OrthoFinder finds orthogroups in a set of proteomes 7
PASS significant transcription factor binding sites from ChIP data 1
Paste two files side by side 1
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 6
QualityScoreDistribution chart quality score distribution 14
Reference Annotation Input An input specifically designed for local Reference Annotations 1
Reheader copy SAM/BAM header between datasets 4
Remove beginning of a file 1
ReorderSam reorder reads to match ordering in reference sequences 17
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Reverse Complement a MAF file 1
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
RmDup remove PCR duplicates 5
SAM-to-BAM convert SAM to BAM 8
sam-to-unsorted.bam converter 1
SamBada Landscape genomic analysis of large datasets for an input file that contains environment and molecular data in one file 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 19
Samtools calmd recalculate MD/NM tags 4
Samtools flagstat tabulate descriptive stats for BAM datset 8
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools split BAM dataset on readgroups 5
Samtools stats generate statistics for BAM dataset 7
Scale Image Scales image 3
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression Filtering 3
Select first lines from a dataset Filtering 4
Select last lines from a dataset 2
Select random lines from a file 2
Send to cloud 1
SFF converter 1
Slice BAM by genomic regions 5
Slice VCF to get data from selected regions 1
smi-to-mol converter 2
smi-to-smi converter 2
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL2 2
SMILES to SDF 2
SNP quality filtering. Step 1 (part 1): Missigness per individual list 1
SNP quality filtering. Step 1 (part 2): Missigness per individual sorted list 1
SNP quality filtering. Step 1 (part 3): Missigness per individual, individual selection 1
SNP quality filtering. Step 1 (part 4): Missigness per individual, filtering 1
SNP quality filtering. Step 2: Minor allele count per marker 1
SNP quality filtering. Step 3: Minimum quality score 1
SNP quality filtering. Step 4: Minimum reads per marker 1
SNP quality filtering. Step 5: Missingness per marker 1
SNP quality filtering. Step 6: Minimum allele frequency 1
SNP quality filtering. Step 7: Hardy-Weinberg equilibrium 1
SNP quality filtering. Step 8: Mendelian errors (for family-based data only) 1
SNP quality filtering. Step 9: Linkage disequilibrium (retain only independent SNPs for further population structure analysis) 1
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift Extract Fields from a VCF file into a tabular file 7
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 8
SnpSift Variant Type Annotate with variant type 8
SnpSift vcfCheck basic checks for VCF specification compliance 8
Sort data in ascending or descending order Sorting 3
SortSam sort SAM/BAM dataset 14
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 17
StringTie merge transcripts 11
Subset columns from a VCF dataset 1
Summary Statistics for any numerical column 3
tabular-to-csv converter 1
tar-to-directory converter 2
toolfactory Scripts into tools v2.0 1
Trim leading or trailing characters 2
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
Upload File from your computer Query and retrieval 3
ValidateSamFile assess validity of SAM/BAM dataset 15
VCF to MAF Custom Track for display at UCSC 2
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 5
VCFtools The vcftools program is intended for analysis of diploid SNP data in VCF format. 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2