BOL

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...

This one is very nice tutorial https://web.stanford.edu/class/cs124/lec/med.pdf

Why are de Bruijn #graphs useful for #genome #assembly? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5531759/

There are other popular measures of edit distance, which are calculated using a different set of allowable edit operations. For instance, the Damerau–Levenshtein distance allows insertion, deletion, substitution, and...

If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomics

Comparative genomics educational material and papers bookmarks https://github.com/iansealy/coursera-comparinggenomes

ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...

Store all files in a array using perl: my @filesbwa = <$base_name/reads/$base_name.$library.bwa.*fa> #Store #Keep #Array #Perl

I recently used ABySS new program "abyss-mergepairs", source code https://github.com/bcgsc/abyss/blob/master/Align/mergepairs.cc You can also try USEARCH https://academic.oup.com/bioinformatics/article/31/21/3476/194979 Hope useful.

I want to merge PE reads. Can you please suggest me good tools.

#Error filtering, pair assembly and error #correction for next-generation sequencing #reads https://academic.oup.com/bioinformatics/article/31/21/3476/194979

Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...

HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not...

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...

Common usage  SPAdes: de Bruijn graph based assembler The last assembler we will run is SPAdes. SPAdes is different from the other assemblers in that it generates a final assembly from multiple kmers. A list of kmers is...

Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a...