BOL

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of...

#Short #read #alignment: an #introduction https://www.sevenbridges.com/short-read-alignment-algorithms/

BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous...

We now need to install the poRe dependencies in R, which is very easy: R source("http://www.bioconductor.org/biocLite.R") biocLite("rhdf5") install.packages(c("shiny","bit64","data.table","svDialogs")) q() R may ask if you want...

 use SPAdes to assemble the data.  SPAdes is a swiss-army knife of genome assembly tools, and by default includes read correction.  This takes up lots of RAM, so we are going to skip it.  We will also only use 3 kmers to save...

I recommend to have a look at this BOL  For De-novo Genome Assembly -- Canu. Flye and MARVEL sound promising.Alignment -- minimap2 and/or LAST, depending on the application. LAST is particularly good...

bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...

Canu is one of the best de novo assemblers available for long reads - it’s a fork and updated version of the Celera assembler that was used to assemble the human genome. It is quite a complex beast that has HPC integration built in -...

I followed this to assemble the genome using ONT (nanopore reads) 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...

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454....

we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a...

#N50 = contig length so that half of the contigs are longer and 1/2 of contigs are shorter

Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an...

This made me think of Perl https://benchmarksgame-team.pages.debian.net/benchmarksgame/faster/perl.html . #PerlLove