Run Maq Now

Follow these steps to try Maq. All you need is a reference sequence file in the FASTA format.

1. Prepare a reference sequence (ref.fasta). Better a bacterial genome.
2. Download maq, maq-data and maqview at the download page.
3. Copy maq, maq.pl and maq_eval.pl to the $PATH or to the same directory.
4. Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go:

   maq.pl demo ref.fasta calib-30.dat
   

   where calib-30.dat is contained in maq-data.
5. View the alignment:

   cd maqdemo/easyrun;
   maqindex -i -c consensus.cns all.map;
   maqview -c consensus.cns all.map

Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.

Address of the bookmark: http://maq.sourceforge.net

• paired-end (PE) and/or mate-pair libraries (NGS-based mode)
• long reads (NGS-based mode)
• synteny to the genome of some related species (reference-based mode)

Scaffolding 

In reference-based mode, pyScaf uses synteny to the genome of closely related species in order to order contigs and estimate distances between adjacent contigs.

Contigs are aligned globally (end-to-end) onto reference chromosomes, ignoring:

• matches not satisfying cut-offs (--identity and --overlap)
• suboptimal matches (only best match of each query to reference is kept)
• and removing overlapping matches on reference.

In preliminary tests, pyScaf performed superbly on simulated heterozygous genomes based on C. parapsilosis (13 Mb; CANPA) and A. thaliana (119 Mb; ARATH) chromosomes, reconstructing correctly all chromosomes always for CANPA and nearly always for ARATH (Figures in dropbox, CANPA table, ARATH table).
Runs took ~0.5 min for CANPA on 4 CPUs and ~2 min for ARATH on 16 CPUs.

Important remarks:

• Reduce your assembly before (fasta2homozygous.py) as any redundancy will likely break the synteny.
• pyScaf works better with contigs than scaffolds, as scaffolds are often affected by mis-assemblies (no de novo assembler / scaffolder is perfect...), which breaks synteny.
• pyScaf works very well if divergence between reference genome and assembled contigs is below 20% at nucleotide level.
• pyScaf deals with large rearrangements ie. deletions, insertion, inversions, translocations. Note however, this is experimental implementation!
• Consider closing gaps after scaffolding.

Address of the bookmark: https://github.com/lpryszcz/pyScaf

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

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

Further information about LACHESIS, including source code, documentation and a user's guide are available at: http://shendurelab.github.io/LACHESIS.

Manuscript describing LACHESIS was published as: Burton JN#, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.272. PubMed PMID: 24185095.

http://shendurelab.github.io/LACHESIS/

Address of the bookmark: http://shendurelab.github.io/LACHESIS/

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

Address of the bookmark: http://mgra.cblab.org/

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Address of the bookmark: http://genomicus.biologie.ens.fr/genomicus-90.01/cgi-bin/search.pl

Address of the bookmark: https://github.com/reubwn/hgt

Address of the bookmark: https://sourceforge.net/projects/ksnp/files/