hal.archives-ouvertes.fr - Pros and cons of HairSplitter Limitations of HairSplitter:
Not very fast: it re-polishes the whole assembly
Limited in the number of haplotypes
Strengths of HairSplitter:
Very modular, can be used with any assembler
Naive: makes no...
bioen-compbio.bioen.illinois.edu - Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end...
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 - 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...
bioinformatics.oxfordjournals.org - Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a...
github.com - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomesMads...
www.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...
www.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...
musket.sourceforge.net - 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...
github.com - Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and...