How to interpret a contig statistics table? · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

How to interpret a contig statistics table?

I am new to WGS assembly. Sequencing company has given me a denovo assembly report. It contains a table looks like the following https://ibb.co/G3cfkN8 . Could you please explain me how to interpret it? What I have right now are contigs. Can you please point me to a reference paper regarding this? if I have N100 contigs, does that mean I do not need any scaffolds for gene prediction?

ContigStat table

assembly wgs n50 contigs soapdenovo2

• 1,250 views • link

written 6.1 years ago by mrj •

How to add images to a Biostars post

• 0 views • link

written 6.1 years ago by Asaf

0 answers

No answers yet.

Log in to answer this question.

More posts like this

is quality evaluation of transcriptome assembly still required if my workflow is (good quality read…
written 5.4 years ago by mrj •

I am working on a RNA-seq analysis of mice. My workflow is as follows. 1. quality filtering of reads 2. using bowtie2-build to index my …
Contigs have different mutations than raw reads
written 5.8 years ago by Rashedul Islam

Hi, I ran two assembly softwares and called mutations from the contigs. However, when I compared the contigs with raw reads, I found some instances …
Which fasta files are assembled transcripts IDBA_tran assembler ?
written 6.2 years ago by sunnykevin97

Hi I used IDBA_tran denovo assembler for RNA_seq assembly. After assembly I generated lot of files ? 1)contig.fa for 20,30,40,50,60 kmer's , filesize - 115M,...120M …
IBD probablity for each Genotype pair
written 7.5 years ago by cetin.m

I am trying to understand the below table from the lcmlkin paper, (Lipatov 2015). It shows the genotype pairs and the probabilities of having 0, …
How I can visualize my GO term data in excel?
written 8.7 years ago by uk0gam •

Hello I got the GO term data thought de novo from the RNA-seq company. but company give me the data only excel form. So I …
dedupe.sh from bbmap excludes contigs with insufficient overlap
written 9.1 years ago by biomagician

Hi, I am using the following command: grep '>' celegans.fa | wc -l >> numberOfContigsBefore.txt dedupe.sh -Xmx28g in=celegans.fa out=merged.fa minoverlap=100000000 maxedits=50 minidentity=98 overwrite=t > mergedNotes.txt …
jModelTest - Interpreting its outputs
written 9.1 years ago by Neuls •

Hi, I ran jModeltest program in order to choose the model that best fits my data using different selection criteria (AIC, BIC..). I'm having trouble …
Genome assembly tools
written 9.7 years ago by Clarancia •

My objective is to mine [SSR][1] from the genome sequences. But all i have is only scaffolds and contigs data about the organisms. Please suggest …
Assembling a chromosome for an E. coli strain using contigs/scaffolds from two WGS projects
written 11.1 years ago by rnnh •

<p>Hello everyone,</p> <p>I'm working on improving the gene coverage for the chromosome of an <em>E. coli</em> strain, using existing WGS data. There are two WGS …
Minimum Or Optimal Rpkm Value To Find If A Transcript Is Significant
written 14.5 years ago by Prakki Rama

<p>Hello all,</p> <p>Could i please know:</p> <ol> <li><p>Does a high RPKM value always report that the transcript is significant? How far is it reliable? If …