mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Please send your questions and comments to mchakrab@uci.edu.

Citation https://www.nature.com/articles/s41588-017-0010-y

Address of the bookmark: https://github.com/mahulchak/mscaffolder

More at http://www.cmdn.org.np/main/index.php

• 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

minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta
nucmer -p nucmer assembly.fasta racon_assembly.fasta
show-snps -C -T -r nucmer.delta

This reports Racon's changes in a table. You can exclude indels with the -I option in show-snps. 

This process (Racon -> MUMmer -> SNP table) solves the problem I originally raised in this issue. So as far as I'm concerned, you can close this issue (or keep it open if you still want to implement some kind of variant table).

CSIR-IICT is conducting Walk in Interview for the following position on a purely temporary basis for the sponsored project "GENESIS (BSC-0121) at 10.00 AM on 19th August 2014 at IICT, Hyderabad

Position : Research Associate
No of Post : One
Desired Profile : PhD in computation biology or M.Tech in Computational Biology with three years experience in relevant subject and atleast one research paper in SCI journal

Experience : Knowledge in vector and vector borne disease, disease modeling, GIS mapping and modeling.
Age : 35 years
Stipend : Rs 22000/- + HRA

Eligible candidate may download the application form from our website http://www.iictindia.org and appear for interview along with the duly filled in application form supported by bio-data and one set of attested photo copies of certificates of educational qualification, age, experience, caste, latest photograph and the cadndidates are required to bring all the original certificates for verification

Walk in Interview : 19.08.14

Applications are invited for the post of Junior Research Fellow (JRF) in a DBT funded IYBA project entitled “Generatingaprotein-ncRNA interactome for Dorsal mediated gene regulation and dorso-ventral patterning genes in Drosophila” in the Lab. Of Molecular Biology at the Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi. The project requires extensive use of molecular, genetic and genomic approaches.

POST: Junior Research Fellow (JRF)

NO. OF VACANCIE(S) - (01)

FELLOWSHIP: Rs. 16,000/- plus HRA

PROJECT DURATION: 2014-2016 (Two years)

LAST DATE FOR APPLICATION: Aug 18, 2014.

Eligibility criteria:

M.Sc./M.Tech./ in Biological Sciences/Biotechnology/Bio-Informatics. Candidates with research experience in the field of Drosophila/Yeast genetics will be preferred.

Application Procedure:

A covering letter along with your CV, copy of prior publications (if any) and proof of experience should be e-mailed to lmb_sau@aol.com. Hardcopy of the application should be brought on the day of interview along with other testimonials and marks statements for verification purpose.

IMPORTANT NOTE:

-No TA/DA will be paid for attending the interview.

-SAU may select candidates against the post depending upon qualification and experience of candidates and reserves the right to relax any of the qualifications in case the candidate is found otherwise well qualified by the Selection Committee

-The abovementioned post is temporary and will be initially offered for a period of one year and can be extended, on satisfactory performance.

More at http://www.sau.ac.in/recruitment/vacancy.html

Eligibility : MSc, M Phil / Phd, BE/B.Tech
Location : Himachal Pradesh-other
Job Category : Govt Jobs, Research, Walkin
Last Date : 20 Aug 2014

Advertisement No.6/2014

Post : Project Fellow
Research Associate/ Project Fellow Jobs opportunity in CSIR-Institute of Himalayan Bioresource Technology
M.Sc. in Bioinformatics/Computer Science with 55% marks and (ii) M.Sc. Bioinformatics/ Computational biology/ P.G. Diploma in Bioinformatics/B.Tech. or higher Degree in Bioinformatics with 55% marks

Date of Interview: 29.08.2014.

More at http://www.ihbt.res.in/recruit/AdvtNo6_2014.pdf