Recently published apps

We have published the following new and updated apps in our Public Apps gallery:

• ABySS 2.3.5 – a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
• Minia 3.2.6 – a short-read assembler based on a de Bruijn graph.
• IDBA 1.1.3 toolkit:
  • IDBA-Hybrid – a de novo assembler for hybrid sequencing data.
  • IDBA-UD – a short-read-data de novo assembler.
  • fq2fa – used for converting FASTQ format read data to FASTA format suitable for IDBA tools.
• ABACAS 1.3.1 – used for contiguating reference-based assemblies.
• Viralrecon Illumina De novo assembly workflow – designed for amplicon and metagenomics short-reads assembly. It is able to analyze metagenomics data obtained from shotgun sequencing (e.g. directly from clinical samples) and enrichment-based library preparation methods (e.g. amplicon-based or probe-capture-based data). It takes single or multiple sample Illumina short-reads, and performs reads trimming, removing host reads, assembly with one of the five included assemblers, blasting and different QC metrics calculating.
• Picard 3.0.0 toolkit:
  • Picard CollectMultipleMetrics – collects BAM statistics by running multiple Picard modules at once.
  • Picard ValidateSamFile validates an alignments file against the SAM specification.
  • Picard SortSam – sorts alignment files (BAM or SAM).
  • Picard RevertSam – reverts a BAM/SAM file to a previous state.
  • Picard MarkDuplicates – marks duplicate reads in alignment files.
  • Picard GenotypeConcordance – calculates genotype concordance between two VCF files.
  • Picard GatherBamFiles – merges BAM files after a scattered analysis.
  • Picard FixMateInformation – verifies and fixes mate-pair information.
  • Picard FastqToSam – converts FASTQ files to an unaligned SAM or BAM file.
  • Picard CrosscheckFingerprints – checks a set of data files for sample identity.
  • Picard CreateSequenceDictionary – creates a DICT index file for a sequence.
  • Picard CollectWgsMetricsWithNonZeroCoverage – evaluates the coverage and performance of WGS experiments.
  • Picard CollectVariantCallingMetrics – can be used to collect variant call statistics after variant calling.
  • Picard CollectSequencingArtifactMetrics – collects metrics to quantify single-base sequencing artifacts.
  • Picard CollectHsMetrics – collects hybrid-selection metrics for alignments in SAM or BAM format.
  • Picard CollectAlignmentSummaryMetrics – produces a summary of alignment metrics from a SAM or BAM file.
  • Picard CheckFingerprint – checks sample identity of provided data against known genotypes.
  • Picard BedToIntervalList – converts a BED file to a Picard INTERVAL_LIST format.
  • Picard AddOrReplaceReadGroups – assigns all reads to the specified read group.
• SnpEff 5.1d toolkit:
  • SnpSift Filter – filters SnpEff-annotated VCF files using arbitrary expressions.
  • SnpEff – which is a variant annotation and effect prediction tool.
  • SnpSift Annotate – which annotates VCF files.
  • SnpSift dbNSFP – which allows annotation with dbNSFP (an integrated database of functional predictions from multiple algorithms, including SIFT, Polyphen2, LRT, MutationTaster, PhyloP and GERP++).

Marko Marinkovic