A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2021-05-18, 21:36
based on data in:
/mnt/c/Users/paule/Documents/VGEA/results
General Statistics
Showing 2/2 rows and 7/10 columns.Sample Name | M Reads Mapped | N50 (Kbp) | Length (Mbp) | % Duplication | GC content | % PF | % Adapter |
---|---|---|---|---|---|---|---|
CV18 | 0.0 | 29.9Kbp | 0.0Mbp | 38.5% | 50.2% | 99.7% | 2.2% |
CV29 | 0.0 | 30.0Kbp | 0.0Mbp | 30.9% | 45.7% | 99.3% | 0.3% |
QUAST
QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.
Assembly Statistics
Sample Name | N50 (Kbp) | N75 (Kbp) | L50 (K) | L75 (K) | Largest contig (Kbp) | Length (Mbp) | Misassemblies | Mismatches/100kbp | Indels/100kbp | Genome Fraction |
---|---|---|---|---|---|---|---|---|---|---|
CV18 | 29.9Kbp | 29.9Kbp | 0.0K | 1.0K | 29.9Kbp | 0.0Mbp | 0.0 | 33.52 | 0.00 | 99.8% |
CV29 | 30.0Kbp | 30.0Kbp | 0.0K | 1.0K | 30.0Kbp | 0.0Mbp | 0.0 | 23.59 | 0.00 | 99.2% |
Number of Contigs
This plot shows the number of contigs found for each assembly, broken down by length.
Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.
Samtools Flagstat
This module parses the output from samtools flagstat
. All numbers in millions.
fastp
fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
Filtered Reads
Filtering statistics of sampled reads.
Duplication Rates
Duplication rates of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.