BOL

Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/30/18/2559/2475628
Reference-free SNP detection: dealing with the data deluge

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083407/
GATB/DiscoSnp: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

https://github.com/GATB/DiscoSnp
De novo assembly | Oxford Nanopore Technologies

https://nanoporetech.com/taxonomy/term/131
De novo long-read assembly of a complex animal genome | bioRxiv

https://www.biorxiv.org/content/early/2017/09/10/187054
Rapid de novo assembly of the European eel genome from nanopore sequencing reads | Scientific Reports

https://www.nature.com/articles/s41598-017-07650-6.epdf?author_access_token=dktG7e98wyRJnaEEMTcPqtRgN0jAjWel9jnR3ZoTv0P7E7t-wVGo30iojNO7dICajNY_7PE5xVPv6OoLe7hn9TeUjcZ5umREOzNoPMWkfYH58RS6uxm3vm4e4BG2AA_WKW84i6egKK271NwMq-NfzA%3D%3D
nanoporetech/ont-assembly-polish: ONT assembly and Illumina polishing pipeline

https://github.com/nanoporetech/ont-assembly-polish
Generade-nl/TULIP: TULIP - The Uncorrected Long read Itegration Pipeline

https://github.com/Generade-nl/TULIP
www.nature.com

https://www.nature.com/articles/s41598-017-03996-z
Example gallery of NanoPlot – Gigabase or gigabyte

https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/
Tool documentation

https://broadinstitute.github.io/picard/command-line-overview.html
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. - PubMed - NCBI

https://www.ncbi.nlm.nih.gov/pubmed/24185095
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html
Measuring the distance between multiple sequence alignments | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/28/4/495/212883
The MUMmer 3 examples

http://mummer.sourceforge.net/examples/
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/tips.html
Omega | Overlap-graph de novo Assembler for Metagenomics

https://omega.omicsbio.org/
abiswas-odu/Disco: Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler

https://github.com/abiswas-odu/Disco
SAGE: String-overlap Assembly of GEnomes | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-302

Fast and sensitive mapping of nanopore sequencing reads with GraphMap | Nature Communications

https://www.nature.com/articles/ncomms11307
lumpy-sv/extractSplitReads_BwaMem at master · arq5x/lumpy-sv

https://github.com/arq5x/lumpy-sv/blob/master/scripts/extractSplitReads_BwaMem
jts/nanocorrect: Experimental pipeline for correcting nanopore reads

https://github.com/jts/nanocorrect

video - how to install flash plugin on ubuntu 14.04 LTS 64-bit version - Ask Ubuntu

https://askubuntu.com/questions/469553/how-to-install-flash-plugin-on-ubuntu-14-04-lts-64-bit-version
lh3/fermi: A WGS de novo assembler based on the FMD-index for large genomes

https://github.com/lh3/fermi
Multi-metagenome

http://madsalbertsen.github.io/multi-metagenome/docs/step9.html
Bandage by rrwick

https://rrwick.github.io/Bandage/
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/30/15/2210/2391162
Genome Architecture and Evolution of a Unichromosomal Asexual Nematode - ScienceDirect

https://www.sciencedirect.com/science/article/pii/S096098221731076X?via%3Dihub#fig4
How to determine chimeras in my de novo assembly? - SEQanswers

http://seqanswers.com/forums/showthread.php?t=26721
samtools(1) manual page

http://www.htslib.org/doc/samtools.html
How To Filter Mapped Reads With Samtools

https://www.biostars.org/p/56246/
The MUMmer 3 manual

http://mummer.sourceforge.net/manual/#nucmer
assembly_olc.pdf

http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf
SAM and BAM filtering oneliners

https://gist.github.com/davfre/8596159
Inroduction to dot-plots

http://www.code10.info/index.php%3Foption%3Dcom_content%26view%3Darticle%26id%3D64:inroduction-to-dot-plots%26catid%3D52:cat_coding_algorithms_dot-plots%26Itemid%3D76
RepeatFinder Home Page

http://www.cbcb.umd.edu/software/RepeatFinder/
RepeatFinderReprint.pdf

http://www.cbcb.umd.edu/software/RepeatFinder/RepeatFinderReprint.pdf
https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html
Circular Visualization in R

http://zuguang.de/circlize_book/book/introduction.html#a-qiuck-glance
Creating a coverage plot using BEDTools and R

https://davetang.org/muse/2015/08/05/creating-a-coverage-plot-using-bedtools-and-r/
Eval: A software package for analysis of genome annotations | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-50
eval-documentation.pdf

http://mblab.wustl.edu/media/software/eval-documentation.pdf
OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921174/
sequence - download.tardigrades.org > v1 > sequence

http://download.tardigrades.org/v1/sequence/
ksahlin/BESST: BESST - scaffolder for genomic assemblies

https://github.com/ksahlin/BESST
reubwn/scripts: Useful scripts for various things

https://github.com/reubwn/scripts
ICEberg

http://db-mml.sjtu.edu.cn/ICEberg/index.php
Satsuma - Evolution and Genomics

http://evomics.org/learning/genomics/satsuma/
A complete bacterial genome assembled de novo using only nanopore sequencing data | Nature Methods

https://www.nature.com/articles/nmeth.3444
vezzi/FRC_align: Computes FRC from SAM/BAM file and not from afg files

https://mail.google.com/mail/u/0/#inbox
Read GTF file into R - Dave Tang's blog

https://davetang.org/muse/2017/08/04/read-gtf-file-r/

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html
Dot: Interactive dot plot for genome-genome alignments

https://dnanexus.github.io/dot/
Zoho Accounts

https://accounts.zoho.eu/signin?servicename=ZohoProjects&serviceurl=https%3A%2F%2Fprojects.zoho.eu%2Fportal%2Favaga2
lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences

https://github.com/lh3/minimap2
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-211
Palindromic gene amplification — an evolutionarily conserved role for DNA inverted repeats in the genome | Nature Reviews Cancer

https://www.nature.com/articles/nrc2591
bioinformatics - BLAST DNA Sequences Reversed - Biology Stack Exchange

https://biology.stackexchange.com/questions/8160/blast-dna-sequences-reversed
LASTZ

http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
SOGo - (1652) Inbox

https://sogo.unamur.be/SOGo/so/jnarayan/Mail/view
Tetra-Nucleotide Analysis (TNA) | BIOiPLUG Help center

http://help.bioiplug.com/tetra-nucleotide-analysis-tna/

Clustering metagenomic contigs on tetranucleotide frequency — CGAT documentation

http://cgat.readthedocs.io/en/latest/recipes/metagenome_contigs_kmers.html