https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

• hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting.
• gcp: K-mer GC Processor. Creates a matrix of the number of K-mers found given a GC count and a K-mer count.
• comp: K-mer comparison tool. Creates a matrix of shared K-mers between two (or three) sequence files or hashes.
• sect: SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.
• blob: Given, reads and an assembly, calculates both the read and assembly K-mer coverage along with GC% for each sequence in the assembly.SEquence Coverage estimator Tool.
• filter: Filtering tools. Contains tools for filtering k-mer hashes and FastQ/A files:
  • kmer: Produces a k-mer hash containing only k-mers within specified coverage and GC tolerances.
  • seq: Filters a sequence file based on whether or not the sequences contain k-mers within a provided hash.
• plot: Plotting tools. Contains several plotting tools to visualise K-mer and compare distributions. The following plot tools are available:
  • density: Creates a density plot from a matrix created with the "comp" tool. Typically this is used to compare two K-mer hashes produced by different NGS reads.
  • profile: Creates a K-mer coverage plot for a single sequence. Takes in fasta coverage output coverage from the "sect" tool
  • spectra-cn: Creates a stacked histogram using a matrix created with the "comp" tool. Typically this is used to compare a jellyfish hash produced from a read set to a jellyfish hash produced from an assembly. The plot shows the amount of distinct K-mers absent, as well as the copy number variation present within the assembly.
  • spectra-hist: Creates a K-mer spectra plot for a set of K-mer histograms produced either by jellyfish-histo or kat-histo.
  • spectra-mx: Creates a K-mer spectra plot for a set of K-mer histograms that are derived from selected rows or columns in a matrix produced by the "comp".

In addition, KAT contains a python script for analysing the mathematical distributions present in the K-mer spectra in order to determine how much content is present in each peak.

This README only contains some brief details of how to install and use KAT. For more extensive documentation please visit: https://kat.readthedocs.org/en/latest/

https://academic.oup.com/bioinformatics/article/33/4/574/2664339 

Address of the bookmark: https://github.com/TGAC/KAT

Address of the bookmark: https://github.com/rbturnbull/orthoflow

So far miniasm is in early development stage. It has only been tested on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. Including the mapping step, it takes about 3 minutes to assemble a bacterial genome. Under the default setting, miniasm assembles 9 out of 12 PacBio datasets and 3 out of 4 ONT datasets into a single contig. The 12 PacBio data sets are PacBio E. coli sample, ERS473430, ERS544009, ERS554120, ERS605484, ERS617393, ERS646601, ERS659581, ERS670327, ERS685285, ERS743109 and a deprecated PacBio E. coli data set. ONT data are acquired from the Loman Lab.

For a C. elegans PacBio data set (only 40X are used, not the whole dataset), miniasm finishes the assembly, including reads overlapping, in ~10 minutes with 16 CPUs. The total assembly size is 105Mb; the N50 is 1.94Mb. In comparison, the HGAP3produces a 104Mb assembly with N50 1.61Mb. This dotter plot gives a global view of the miniasm assembly (on the X axis) and the HGAP3 assembly (on Y). They are broadly comparable. Of course, the HGAP3 consensus sequences are much more accurate. In addition, on the whole data set (assembled in ~30 min), the miniasm N50 is reduced to 1.79Mb. Miniasm still needs improvements.

Miniasm confirms that at least for high-coverage bacterial genomes, it is possible to generate long contigs from raw PacBio or ONT reads without error correction. It also shows that minimap can be used as a read overlapper, even though it is probably not as sensitive as the more sophisticated overlapers such as MHAP and DALIGNER. Coupled with long-read error correctors and consensus tools, miniasm may also be useful to produce high-quality assemblies.

Minimap and miniasm are ultrafast tools for (i) mapping and (ii) assembly. Designed for long, noisy reads, they do not have a correction or consensus step, and therefore the resulting assemblies are contiguous (i.e. long) but very noisy (i.e. full of errors)

We start with an all against all comparison:

minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz

Then we can assemble

miniasm -f reads.fq reads.paf.gz > reads.gfa

Convert GFA to FASTA:

awk '/^S/{print ">"$2"\n"$3}' reads.gfa | fold > reads.fa

And then count how many contigs:

grep ">" reads.fa | wc -l

# Download sample PacBio from the PBcR website
wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | tar zxf -
ln -s selfSampleData/pacbio_filtered.fastq reads.fq
# Install minimap and miniasm (requiring gcc and zlib)
git clone https://github.com/lh3/minimap && (cd minimap && make)
git clone https://github.com/lh3/miniasm && (cd miniasm && make)
# Overlap
minimap/minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz
# Layout
miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa

Address of the bookmark: https://github.com/lh3/miniasm

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

• Mac OS X 10.11.1
• Mac OS X 10.10.3
• Ubuntu 14.04 LTS

Address of the bookmark: https://github.com/mculinovic/EAGLER

python finisherSC.py destinedFolder mummerPath

If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.

python finisherSC.py -par 20 destinedFolder mummerPath

Sometimes, if the names of raw reads and contigs consists of special characters/formats, FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command.

    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' raw_reads.fasta > newRaw_reads.fasta
    cp newRaw_reads.fasta raw_reads.fasta
    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' contigs.fasta > newContigs.fasta
    cp newContigs.fasta contigs.fasta

Address of the bookmark: https://github.com/kakitone/finishingTool

I made Rebaler for bacterial genomes (specifically for the task of testing basecallers). It should in principle work for non-bacterial genomes as well, but I haven't tested it.

Address of the bookmark: https://github.com/rrwick/Rebaler

Address of the bookmark: https://github.com/SUwonglab/COSINE

./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa

Address of the bookmark: https://github.com/ruanjue/wtdbg2