Results for "Illumina"


  • Illuminating next generation sequencing data with Go

    Another good lecture for Illumina sequencing data analysis from  Dan Kortschak, Bioinformatics Group, School of Molecular and Biomedical Science ,The University of Adelaide

    Tags: Illumina, sequencing, discordant read pairs, structural variation

    1340 days ago

  • RNA-Seq De novo Assembly Using Trinity

    Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied seq...

    Tags: Bioinformatics, NGS, RNA-seq, Assembly, Trinity, Illumina

    397 days ago

  • PAired-eND Assembler for DNA sequences

    PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.   More at

    Tags: Bioinformatics, NGS, Assembly, Paired-End, PANDASEQ, Illumina

    383 days ago

  • Sequence assembly with MIRA 4

    MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by electrophoresis sequencing (aka Sanger sequencing) 454 pyro-sequencing (GS20, FLX or Titanium) Ion Torrent Solexa (Illumina) sequencing ...

    Tags: Bioinformatics, NGS, Assembly, Paired-End, MIRA, Illumina

    383 days ago

  • Trimmomatic: A flexible read trimming tool for Illumina NGS data

    Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 ...

    Tags: Bioinformatics, Trim, NGS, Illumina, Reads, Trimmomatic

    374 days ago

  • SPAdes

    SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau...

    Tags: Bioinformatics, NGS, Assembly, Assembler, SPAdes, Reads, Illumina

    370 days ago


    PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable region of the 16S gene, or the constant regions aro...

    Tags: Bioinformatics, Assembly, PANDASEQ, Genome, NGS, Illumina

    91 days ago

  • LoRDEC: a hybrid error correction program for long, PacBio reads

    LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and ...

    Tags: Bioinformatics, LoRDEC, Hybrid, Error, Correction, Program, Long, PacBio, Reads, Illumina

    14 days ago