BOL

cutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...

github.com - In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would not have been possible without the help of many people who...

github.com - Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing...

journals.plos.org - Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for...

Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

drive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW.  UPARSE >OTU clustering for 16S and other marker genes....

github.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)

ftp.genomics.org.cn - 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...

cab.spbu.ru - QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we...

murasaki.dna.bio.keio.ac.jp - Murasaki is an anchor alignment program that is exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes)) scalable (Arbitrarily parallelizable across multiple...