Examples : samtools, bed, topic:conversion

256 tool(s) found

Tool Description Topics Available version(s)
16S rRNA Search Similarity Search 1
Add column to an existing dataset 3
AddCommentsToBam add comments to BAM dataset 11
AddOrReplaceReadGroups add or replaces read group information 11
AnnotateBed annotate coverage of features from multiple files 17
awk 1
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
BAM to BED converter 21
BAM-to-SAM convert BAM to SAM 8
Bar chart for multiple columns 1
BED to BAM converter 18
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
BEDPE to BAM converter 18
BedToIntervalList convert coordinate data into picard interval list format 11
Bowtie2 align Align reads to db 1
Bowtie2 build Create bowtie2 index for hg38 and phiX174 fasta 1
Boxplot of quality statistics 2
bsfcall Mapping bisulfite-seq reads and calling methylated cytosines 1
CalculateEntropyDiv Calculate entropy 1
Change Case of selected columns 1
CleanSam perform SAM/BAM grooming 11
ClosestBed find the closest, potentially non-overlapping interval 17
ClusterBed cluster overlapping/nearby intervals 17
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
COG Search Similarity Search 1
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 11
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 11
CollectGcBiasMetrics charts the GC bias metrics 11
CollectInsertSizeMetrics plots distribution of insert sizes 11
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 12
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 11
ComMet Detection of differentially methylated regions from bisulfite-seq mapping data 1
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 18
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
Concatenate datasets tail-to-head 1
Convert delimiters to TAB 1
Convert BCF to BCF_BGZIP 1
Convert BCF_BGZIP to BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to len file 1
Convert FASTA to Tabular 1
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to interval 2
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
Count occurrences of each record 2
Create single interval as a new dataset 1
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 13
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 11
Cuffmerge merge together several Cufflinks assemblies 12
Cut columns from a table 2
Cut Cut sequence 1
Cutadapt Trim adapter 1
Detect_Indels Detect InDels 1
Detect_SNPs Detect SNPs 1
Download and Extract Reads in BAM format from NCBI SRA 12
Download and Extract Reads in FASTA/Q format from NCBI SRA 12
Download and Generate Pileup Format from NCBI SRA 11
Download References Data for Pitagora-Galaxy 1
Downsample SAM/BAM Downsample a file to retain a subset of the reads 11
Edit Header 1
Elapsed time of each job 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 11
Exclude_N_Fastq2 Exclude Ns 1
ExpandBed replicate lines based on lists of values in columns 17
Export to a Local File 2
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
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 17
FastqMcf sequence quality filtering and clipping 2
FastqToSam convert Fastq data into unaligned BAM 14
Filter data on any column using simple expressions Formatting 1
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
Filter GTF data by attribute values_list 1
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
FilterSamReads include or exclude aligned and unaligned reads and read lists 11
FisherBed calculate Fisher statistic between two feature files 17
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 11
FlankBed create new intervals from the flanks of existing intervals 18
Gatk 3.3 binary loader Upload GATK3.3 to Pitagora galaxy system. 1
Gatk 3.3 variant caller GATK 3.3 based variant call system. 1
GATK resource bundle downloader GATK resource bundle downloader. 1
Gene BED To Exon/Intron/Codon BED expander 1
Genome Coverage compute the coverage over an entire genome 18
Get Microbial Data 1
GetFastaBed use intervals to extract sequences from a FASTA file 17
GFF-to-BED converter Conversion 1
Group data by a column and perform aggregate operation on other columns. 3
GroupByBed group by common cols and summarize other cols 17
GTF-to-BEDGraph converter Conversion 1
Import a Local File 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Intersect intervals find overlapping intervals in various ways 17
JaccardBed calculate the distribution of relative distances between two files 17
JellyfishCount Count K-mer 1
JellyfishDump Dump K-mer 1
Join the intervals of two datasets side-by-side Aggregation 5
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 3
LAV to BED Converts a LAV formatted file to BED format 1
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 17
MACS Model-based Analysis of ChIP-Seq 4
MACS14 Model-based Analysis of ChIP-Seq (1.4.2) 5
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 9
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 11
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 8
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 8
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 8
MAF Coverage Stats Alignment coverage information 1
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
MakeWindowsBed make interval windows across a genome 18
Map with BWA for Illumina 4
Map with BWA for SOLiD 3
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 11
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 11
MaskFastaBed use intervals to mask sequences from a FASTA file 17
MeanQualityByCycle chart distribution of base qualities 11
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge Columns together 2
Merge(final) Output final reports 1
Merge_SNPs_/_InDels_data_files Merge SNPs / InDels data files 1
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 11
MergeBED combine overlapping/nearby intervals into a single interval 17
MergeSamFiles merges multiple SAM/BAM datasets into one 11
MetaGeneAnotator find ORFs 1
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
MultiCovBed counts coverage from multiple BAMs at specific intervals 17
Multiple Intersect identifies common intervals among multiple interval files 21
NormalizeFasta normalize fasta datasets 11
NucBed profile the nucleotide content of intervals in a FASTA file 17
OverlapBed computes the amount of overlap from two intervals 17
Paste two files side by side 1
PhixRemove Remove phiX174 1
Qual_Filter_FASTQFASTA Quality filter 1
QualityScoreDistribution chart quality score distribution 11
RandomBed generate random intervals in a genome 18
RefSeq Search Similarity Search 1
ReldistBed calculate the distribution of relative distances 17
Remove beginning of a file 1
ReorderSam reorder reads to match ordering in reference sequences 14
ReplaceSamHeader replace header in a SAM/BAM dataset 14
Report(interim) Output interim reports 1
Reverse Complement a MAF file 1
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 11
RevertSam revert SAM/BAM datasets to a previous state 11
RNAmmer 1.2 find rRNAs 1
RSEM calculate expression RNA-Seq by Expectation-Maximization 1
RSEM prepare reference 1
RSEM trinity fasta to gene map extract transcript to gene map from trinity 2
Sailfish transcript quantification from RNA-seq data 1
SAM-to-BAM convert SAM to BAM 11
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 14
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 1
sed 1
Select lines that match an expression 1
Select first lines from a dataset 1
Select last lines from a dataset 1
Select random lines from a file 2
SFF converter 1
ShuffleBed randomly redistrubute intervals in a genome 18
SICER Statistical approach for the Identification of ChIP-Enriched Regions 2
SlopBed adjust the size of intervals 18
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
SnpEff Variant effect and annotation 1
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 7
SnpSift Variant Type Annotate with variant type 7
SnpSift vcfCheck basic checks for Vcf specification compliance 7
Sort data in ascending or descending order 2
SortBED order the intervals 17
SortSam sort SAM/BAM dataset 11
Split MAF blocks by Species 1
SQL Runner (SQLite) 1
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
SubtractBed remove intervals based on overlaps 17
Summary Statistics for any numerical column 3
Tabular to CSV converter 1
TagBed tag BAM alignments based on overlaps with interval files 17
TopHat Gapped-read mapper for RNA-seq data 12
TrEMBL Search Similarity Search 1
Trim leading or trailing characters 1
Trinity De novo assembly of RNA-Seq data Using Trinity EST assembly 5
tRNAscan-SE 1.23 find tRNAs 1
Unannotated Extract not annotated sequences 1
Upload File from your computer 2
ValidateSamFile assess validity of SAM/BAM dataset 11
VCF to MAF Custom Track for display at UCSC 1
Visualize distribution of DNA polymorphism 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1
WindowBed find overlapping intervals within a window around an interval 17