This script has been modified by others to convert InDels as well, e.g. this by David Eccles

./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>

https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl

https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl

Know of any other open source software for PacBio data? Email us.

Software categories:

• De novo assembly
• Structural Variations Detection
• Reference-based alignment
• Consensus and variant calling
• RNA analysis
• Epigenetic base modifications and methylation
• Barcoding
• Genome Browsers
• Run QC
• Frameworks and APIs

Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.

 Please comment if you know any other long read addembly tutorial.

Address of the bookmark: http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/

Source code for SKESA is freely available at https://github.com/ncbi/SKESA/releases.

Research Paper @ Link

SKESA algorithm are as follows:

Address of the bookmark: https://github.com/ncbi/SKESA/releases

QUAST-LG is included in the QUAST  package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command!

A short list of the new features (see CHANGES for all):

• Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules
• New k-mer-based completeness and correctness metrics
• BUSCO added for enhanced reference-free analysis
• The concept of upper bound assembly (theoretical limits on the assembly completeness and contiguity for a given genome and set of reads)

Address of the bookmark: http://cab.spbu.ru/software/quast-lg/

I have used the following assemblers

• Spades (v. 3.10.1)
• CANU (v. 1.6)
• Unicycler (v. v0.4.1)
• Miniasm (v. 0.2-r137-dirty)

I have used the following mappers

• minimap2 (v. 2.0rc1-r232)
• minimap (v. 0.2-r124-dirty)
• bwa (v. 0.7.12-r1039)

I have used the following polishing tools

• Racon (v. not available)
• Pilon (v. 1.18)
• Nanopolish (v. 0.8.3)

I have used the following tools to assess genome assembly characteristics

• ANI.pl (https://github.com/chjp/ANI)
• CheckM (v. 1.0.7)
• Prokka (v. 1.12)
• QUAST (v. 2.3)
• mummer (v. not available)

If you have any ideas or superior tools we have missed please let us know in the comments.

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals;

Address of the bookmark: http://www.bx.psu.edu/miller_lab/car/

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi