Skewer is an adapter trimming tool specially designed for processing next-generation sequencing (NGS) paired-end sequences. Windowed Adaptive Trimming for FastQ files using quality
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Seq圜lean is a comprehensive preprocessing software application for NGS reads.
PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data The tool is also able to rescue fused reads. Is a tool to identify, orient and trim full-length Nanopore cDNA reads. Pbmarkdup takes one or multiple sequencing chips of an amplified libray as HiFi reads and marks or removes duplicates. Quality control for long reads from ONT (Oxford Nanopore Technologies) sequencing. Starting in SMRT Link v5.1.0, it is the tool that powers the Demultiplex Barcodes GUI-based analysis application. Lima, the PacBio barcode demultiplexer, is the standard tool to identify barcode sequences in PacBio single-molecule sequencing data. LeeHom is a program for the Bayesian reconstruction of ancient DNA The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra. JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. In a few cases, the metric files are produced after a run during secondary analysis (index metrics) or for faster display of a subset of the original data (collapsed quality scores).įunctions for viral amplicon-based sequencing.
These metric files are binary files produced during a run providing detailed statistics about a run.
The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files. This is faster than alignment and can be used for contamination detection.ĬCS is a PacBio tool that generates highly accurate single-molecule consensus reads (HiFi Reads).ĬheckQC is a program designed to check a set of quality criteria against an Illumina runfolder.Īdapter clipping and read merging in ancient DNA analysisĬluster Flow is a simple and flexible bioinformatics pipeline tool.Ĭutadapt is a tool to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.Īn ultra-fast all-in-one FASTQ preprocessorįastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.įastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.įLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from NGS data. Overlapping paired-ended reads can be merged into consensus sequences and adapter sequence can be found for paired-ended data if not known.Īutomatic Filtering, Trimming, Error Removing and Quality Control for fastq data.īcl2fastq can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.īclconvert can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.īioBloom Tools assigns reads to different references using bloom filters. Removes adapter sequences and trims low quality bases from the 3' end of reads. If you would like another to be added, please open an issue.Ĭlick the tool name to go to the MultiQC documentation for that tool. MultiQC currently supports 114 bioinformatics tools, listed below.
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