Results for "reads"
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How to check if fragmented set of assembly is alright ?
I assembled the genome, by fragmenting(split) the read data in TWO set. After assembling both sets, I am just wondering what to do the next? How to validate? Is that everything is going alright? I only use QUAST and it seems OK to me. Any other suggestions? Note: I assembled the genome w...Tags: NGS, Assembly, Fragmented, Split, Reads
2514 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, wi...Tags: Meraculous, De Novo, Genome, Assembly, Short, Paired-End, Reads
2384 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
2382 days ago
What are the best way to merge paired end reads ?
I want to merge PE reads. Can you please suggest me good tools.Tags: Merge, Reads, PE, NGS
2355 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph should appear in fasta format with 1 entry per node...Tags: Jabba, Hybrid, Error, Correction, Long, Sequencing, Reads
1994 days ago
BBTools for bioinformatician !
BBMap.sh Mapping Nanopore reads BBMap.sh has a length cap of 6kbp. Reads longer than this will be broken into 6kbp pieces and mapped independently. Code: $ mapPacBio.sh -Xmx20g k=7 in=reads.fastq ref=reference.fa maxlen=1000 minlen=200 idtag ow int=f qin=33 out=mapped1.sam minratio=0.15...Tags: BBMap, Map, NGS, Reads, Sam, Bam, Contamination, Filtration
2283 days ago
What are the best software options available for nanopore (ONT) reads ?
Tags: ONT, Nanopore, Assembly, Sequencing, Reads, fast
2205 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you u...Tags: GAPPadder, Sensitive, Approach, Closing, Gaps, Draft, Genomes, Short, Sequence, Reads, Genome, Assembly
2196 days ago
