Where can i get library.txt file for SSPACE?
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4.9 years ago
Calvin ▴ 60

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.

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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?

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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

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4.9 years ago
Sej Modha 4.9k

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.

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Entering edit mode
4.9 years ago

This link has details you are looking SSPACE