Results for "abundance"
Bookmarks
Kraken: ultrafast metagenomic sequence classification using exact alignments
...slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which on...minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn....2872 days ago
- ...l Minia command line looks like: ./minia -in reads.fa -kmer-size 31 -abundance-min 3 -out output_prefix Typ...KmerGenie can be used to determine the best k-mer size, minimum abundance of correct k-mers, and genome...
2709 days ago
- +8 more Bookmarks
Top-level pages
Genome Assembly Tools and Software - PART1 !!
...sequencing along a Reference Sequence The abundance of repeat elements in genomes...of reads, KmerGenie first computes the k-mer abundance histogram for many values of...nks 2.2.1 – Transcript Assembler & Abundance Estimator for RNA-Seq Cuff...2689 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-seq data (uses pseudo...io/kallisto/ Sailfish Estimation of isoform abundances from reference sequences and...ent in metagenomic samples and profiles their abundances (uses composition-based appr...2375 days ago
Opportunity posts
Research fellow (PhD candidate) in computational biology – 2 positions
...inent. The Valen group is dedicated to the fundamental question of how transcription and translation is integrated to obtain the desired protein abundance. The recent development of hi...3666 days ago
Bio-Scripts
- ...performs all steps: read filtering, microbe reference alignment, and abundance scoring PathSeqScoreSpar...Step 3: Classifies pathogen-aligned reads and generates abundance scores -------------------...
2079 days ago
Tags
- KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per k-mer, K-mer Abundance Difference (KAD), which indi...
Tags: KAD, Assessing, genome, assemblies, K-mer, assemblies, abundance, Illumina, reads
1420 days ago
- The abundance of a species in a dataset is considered as the fraction of reads that belong to that species. For example, if there is a dataset with 10,000,000 reads and 1,000,000 of them belong to E. coli, then the abundance of E. coli will be 0.1.
Tags: Estimating, Abundance
587 days ago
Comments
- ...les can be either plaintext or gzipped. kallisto quant produces three output files by default: abundances.h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates...
1364 days ago
Comment on "Running Trinity on RNA-seq !"
...f your organism based on your assembled transcripts and the input RNA-Seq data. Such studies might include: Quantifying transcript and gene abundance. This is a prerequisite to ma...2127 days ago
