2226 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...alyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable im...2226 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Comp...2225 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
...millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one...2224 days ago
mScaffolder: A comparative genome scaffolding tool
...older scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes us...the contigs of the candidate genome guided by their alignments to the reference genome. Please send your ques...2203 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # cr...2198 days ago
RNA-seq Analysis Workshop Course Materials
...hly divided into two "types": Reference genome-based - an assembled g...reads to be aligned against the reference genome and significantly impr...ecies (e.g., Hyacinth macaw); Reference genome-free - no genome assem...this lesson we will focus on the Reference genome-based type of RNA seq....2185 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and Pa...long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a...2182 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
...led individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of to...1481 days ago
Nanopolis: polish a genome assembly
...lish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopoli...2162 days ago