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. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an...

github.com - MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs) Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any...

lindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

There are many R software and bioconductor packages for NGS data analysis, some of them are as follows Biostrings The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It...

github.com - Tools to create plots showing N-statistics for genome assemblies More at https://github.com/dentearl/n50PlottingTools

sfu-compbio.github.io - SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any...

bioinf.spbau.ru - SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8,...

http://busco.ezlab.org/ - High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures...

mrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...

hoffmann.bioinf.uni-leipzig.de - segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is...