JVARKIT statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

JVARKIT specifications

Information


Unique identifier OMICS_24364
Name JVARKIT
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format VCF, BED, SAM, BAM, CLUSTAW, FASTA, FASTQ, TBI, BAI
Output format VCF, FASTQ, XML, SAM, BAM, BED, FASTA, PSL, JSON, RDF, GFF
Operating system Unix/Linux
Programming languages Java
License MIT License
Computer skills Advanced
Version KnimeHelper-2017-11-20
Stability Stable
Maintained Yes

Subtools


  • bam2svg
  • bioalcidae
  • bioalcidaejdk
  • biostar77288
  • PcrClipReads
  • sam2tsv
  • sam4weblogo
  • samjdk
  • samjs
  • sigframe
  • vcffilterjdk
  • vcffilterjs

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Pierre Lindenbaum

Additional information


http://lindenb.github.io/jvarkit/

Publication for JVARKIT

JVARKIT citations

 (7)
library_books

Differential 3’ processing of specific transcripts expands regulatory and protein diversity across neuronal cell types

2018
eLife
PMCID: 5898910
PMID: 29578408
DOI: 10.7554/eLife.34042.036

[…] main from protein domain databases (Superfamily, SMART, Pfam and Prosite). Protein modifications were downloaded from Uniprot () and mapped to mm10 using backlocate software (http://lindenb.github.io/jvarkit/). Genomic coordinates of protein modifications were then overlapped with alternative 3’UTR isoforms to find those that are unique to the long isoform.To analyze the relationship between 3’UTR […]

library_books

Linkage of A to I RNA Editing in Metazoans and the Impact on Genome Evolution

2017
Mol Biol Evol
PMCID: 5850729
PMID: 29048557
DOI: 10.1093/molbev/msx274

[…] stical power in detecting linkage of the editing events.For each BAM sequence alignment file, we extracted all the uniquely mapped reads spanning at least two editing sites with SAMtools 1.3.1 () and Sam2Tsv (). Soft clipping bases in the alignments were not considered, and reads spanning only one editing sites were discarded. In each sample, we required the editing sites to have sequencing covera […]

library_books

MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non Model Sequence Data

2017
Biology
PMCID: 5372007
PMID: 28218638
DOI: 10.3390/biology6010014

[…] red scale). The final VCF file containing all the filtered polymorphisms within each ORF and the consensus sequence of each ORF were imported respectively into the Biostars 175929 tool as part of the JVarkit package [] to produce a compressed fasta file database for each amplicon containing generated references sequences with every possible combination of identified polymorphisms (). All generated […]

library_books

A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes

2016
PLoS One
PMCID: 5147911
PMID: 27936026
DOI: 10.1371/journal.pone.0167600

[…] asing was performed with SAMtools [] phase version 0.1.19 on the two sets of extracted records.MiSeq read pairs were extracted and assigned from the MiSeq bam file using a combination of BEDTools and JVarkit git commit 865252a [, ] at the private variants (12 SNPs and 2 INDELs) in the single contributor datasets (). The read pairs were sorted into three pools of extracted reads, being shared, priv […]

library_books

Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single stranded Virus Next generation Sequencing

2015
Mol Ther Nucleic Acids
PMCID: 4881760
PMID: 26506038
DOI: 10.1038/mtna.2015.32

[…] s-mpileup, because the read depth was far too great (> 200,000) for the classical (but more robust) callers. The source code for this java program is available on GitHub at https://github.com/lindenb/jvarkit/wiki/MiniCaller. Essentially, this program uses the java library for BAM (htsjdk) to load a set of BAM files and scans all of the bases in the reference genome from 5′ to 3′; for each position […]

call_split

Whole Genome Sequence Analysis Reveals the Enterovirus D68 Isolates during the USA 2014 Outbreak Mainly Belong to a Novel Clade

2015
Sci Rep
PMCID: 4606740
PMID: 26469882
DOI: 10.1038/srep15223
call_split See protocol

[…] hesis step, were removed. The resulting genome sequences, along with those EV-D68 genomes publicly available in GenBank, were compared using the Clustal X (version 2.1). The biostar94573 algorithm of jvarkit (https://github.com/linden/jvarkit/wiki/biostar94573) was used to generate a variant call format file (.vcf) from the CLUSTAL multi-sequence alignment file (.aln). The vcftools suite was used […]

Citations

Looking to check out a full list of citations?

JVARKIT institution(s)
Institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France

JVARKIT reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review JVARKIT