Question: Where can i get library.txt file for SSPACE?
0
gravatar for Calvin
4.2 years ago by
Calvin60
Australia
Calvin60 wrote:

Hi, i have used SPades to generate contigs file for bacteria genome assembly by using 2x150 illumina paired-end reads. But when i proceed to SSPACE for contig extension, SSPACE requires library.txt as parameter. Moreover, i didnt find any files generated from SPades has this "library.txt". So my question is how can i obtain this library.txt which i believe it must be come from my own paired-end reads.

spades sspace • 3.2k views
ADD COMMENTlink modified 8 months ago by Naomifu0 • written 4.2 years ago by Calvin60

I have 150bp reads in order to eventually find the genome of bacteria. How do I know which Aligner to use (bwa or bowtie)? In addition, how do I find out what is the insert size and the error for the 4th and 5th columns in the library.txt file?

Thank you in advance.

ADD REPLYlink written 8 months ago by Naomifu0

Please do not ask random questions that are unrelated to the topic. Please browse existing threads and if this does not help open a new question following [ Please read before posting a question ] -- How To Ask A Good Question

ADD REPLYlink written 8 months ago by ATpoint38k
3
gravatar for Sej Modha
4.2 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

SSPACE library file is a simple text file with following information in space separated format.

NameTag Aligner(bwa or bowtie) Fastq1 Fastq2 AverageInserSize Error OrientationIndication

A sample command would look like this

Lib1 bwa reads_R1.fq reads_R2.fq 185 0.99 FR

You can use SPAdes scaffolds output in fasta format as input for SSPACE with an option -x=1 to extend the scaffolds.

ADD COMMENTlink written 4.2 years ago by Sej Modha4.7k
3
gravatar for Prasad
4.2 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

This link has details you are looking SSPACE

ADD COMMENTlink written 4.2 years ago by Prasad1.6k
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