Results for "Reference"
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Maq: Mapping and Assembly with Quality
...It builds assembly by mapping short reads to reference sequences. Maq is a project h...ow these steps to try Maq. All you need is a reference sequence file in the FASTA fo...or to the same directory. Simulate diploid reference and read sequences, map reads...2721 days ago
- ...ual genome studied in the experiment and the reference genome of the species. Howeve...ols, this information is disregarded and the reference genome is used. Results. We p...the resulting contigs to generate a modified reference sequence. In this way, it can...
2718 days ago
- ...osen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads, aligns reads to reference sequence(s). All of these ana...
2712 days ago
Standardized velvet assembly report
...ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, add f...2704 days ago
BIMA V3: an aligner customized for mate pair library sequencing
...d for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a challenging and t...2699 days ago
e-RGA: enhanced Reference Guided Assembly of Complex Genomes
...eads. In this paper, we propose a novel method that aims to improve de novo assembly in the presence of a closely related reference. The idea is to combine de novo and reference-guided assembly in order to o...2694 days ago
- ...the genome of some related species (reference-based mode) Scaffolding In reference-based mode, pyScaf uses synte...es (only best match of each query to reference is kept) and removing overla...orks very well if divergence between reference genome and assembled contigs...
2694 days ago
- ...e or contribute by reporting mistakes or sending patches. Language Reference & TutorialsA collection o...ibing, in detail, the various conceptual parts of the language. Type ReferenceIndex of built-in classes and...
2649 days ago
- ...-annotate annotations.bed Options --ideobed, i A bed file of reference contig lengths/chromosome nam...s (description below) --bars, -b Add track annotations --reference, -f Either hg19, or hg38...
2638 days ago
- ...design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to f...ment positions and identify syntenies of assembly contigs against the reference. The output is then processed...
2635 days ago
