Results for "Contamination"
Bookmarks
BIMA V3: an aligner customized for mate pair library sequencing
...ost NGS alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.), and presenc...2698 days ago
- ...assembly from 1,704 human gut samples formed 1,634 genome bins (>200kb) in 3 hours, where 621 genome bins are >50% complete with <5% contamination from other species. Further a...
2616 days ago
- +8 more Bookmarks
Top-level pages
List of Bioinformatics Software Tools for Next Generation Sequencing
...Microdissection for SNP calling; Java based; for disease-control matched samples; uncovers SNPs with low allele frequency by considering alpha contamination Input: BAM (must be sorted a...2908 days ago
Wire posts
News
Webinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016
...an elaborate pipeline that aligns reads, filters poor-quality matches, computes coverage metrics, identifies variants, checks for sample cross-contamination, and emails quality reports -...3011 days ago
- ...exon-exon spanning primers. This makes it less likely that primers specifically designed to amplify transcripts will also amplify genomic DNA contamination in expression assays. See the...
1467 days ago
- +1 more News
Bio-Scripts
- ...(BETA Tool) Tabulates pileup metrics for inferring contamination Pileup...read metrics relevant to structural variant discovery CalculateContamination Calcula...
2074 days ago
Tags
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
2270 days ago
Comments
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...oduced. Does the kmer content look good to you? How much of the kmer “noise” is part of the final assembly? What do you think contamination would look like in the kmer p...1336 days ago
- ...trol tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. QC3 QC3 ...
2136 days ago
