I have assembled genome of my strain of interest. I have the assembly stats in a log file, stats.txt and contig.fa file. I wish to know the stats such as maximum contig size, minimum, average contig size and number of contigs in range of 1 kbp, 10 kbp and all. Is there any script to extract such info. I have already calculated total number of contigs from the file using a command line text. Kindly help me with a script to do so.
Individual nodes in the contig file display some k mer coverage. What exactly does this coverage refer to?
You should try QUAST http://bioinf.spbau.ru/quast. It provides a number of statistics related to assembly quality. You can either upload your assembly to the QUAST web server or download the tool to your computer.
You should try QUAST http://bioinf.spbau.ru/quast. It provides a number of statistics related to assembly quality. You can either upload your assembly to the QUAST web server or download the tool to your computer.
Primarily you should know, what platform you used to generate NGS data, based on the platform , analysis tool can be optimized. Whatever platform may be, use FastQC tool for quality analysis.
K mer coverage refer to the number of k -mers that were maped on this particular contig, especially number of repeated k-mers that fall onto same position during assembly of the contig. K-mers are structures of nucleotides (4 and more bp) which are defined by the assembly program in your supplied reads and used to map your reads onto each other.
I use the command abyss-fac from ABySS. for the contig stats.
For the kmer coverage, you can just use R to generate a graph using the stats file:
>R --no-save --no-restore
>library(plotrix)
>data weighted.hist(data$short1_cov, data$lgth, breaks=0:50)
>dev.off()
Change the "breaks" parameter to change the range of your kmer coverage X axis
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools