Release note
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++).