Results for "Illumina"
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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 AdelaideTags: Illumina, sequencing, discordant read pairs, structural variation
3899 days ago
shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill pr...Tags: shovill, Assemble, bacterial, isolate, genomes, Illumina, paired-end, reads
1210 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
2956 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 https://github.com/neufeld/pandaseqTags: Bioinformatics, NGS, Assembly, Paired-End, PANDASEQ, Illumina
2942 days ago
- 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
2942 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
2933 days ago
- 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
2929 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
2650 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
2573 days ago
QuorUM: An Error Corrector for Illumina Reads
Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read at every base in the genome. These errors make ha...Tags: QuorUM, Error, Corrector, Illumina, Reads
2361 days ago
