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2SNV Quasispecies reconstruction from long reads


Supplementary materials are available here

To run the tool Java Runtime Environment is necessary (http://java.com/en/download/index.jsp)

Software requires aligned reads in MSA format (fasta reads padded to the same length of all entries)

It is possible to convert pairwise aligned SAM(BAM) file to MSA with the help of program b2w (part of ShoRAH assembler)

Recommended aligner for long SMRT reads is BWA

for example:

bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 input.fasta > output.sam

To compress sort and index SAM to BAM(BAI) install samtools

samtools view -b reads.sam > reads.bam
samtools sort reads.bam -o reads.sorted -O bam
samtools index reads.sorted.bam

To run b2w it is not necessary to install whole ShoRAH software, as an alternative one can download C code from github b2w it is not necessary to install whole ShoRAH software, as an alternative one can download C code from github b2w.c and compile it with gcc or any other compartible C-compiler

b2w -w 2300 -i 0 -x 100000 -o aligned.reads.fas reads.sorted.bam ref.fasta ref_name:0:2300

To run 2snv use jar file

java -jar 2snv-1.0.jar aligned.reads.fas 1000 -t 30 -o haplotypes.fa

2SNV is available at 

2SNV releases

For developers source code and instructions 

2SNV on github

DATA

Reference flu1PB.fa

Clones in fasta format available clones.fa

Raw sequencing data have been submitted to the NIH Short Read Archive (SRA) under accession number: BioProject PRJNA284802