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Maq: Mapping and Assembly with Quality
...pping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq...l to the $PATH or to the same directory. Simulate diploid reference and read sequences, map reads, call va...2715 days ago
- Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome...) For the impatient A typical Minia command line looks like: ./minia -in reads.fa -kmer-size 31 -abundance-...
2699 days ago
- ...st of the individual subcommands will take either a single file or a pair of files as input. If no input file is specified, fqtools will attempt to read data from stdin. In this...
2699 days ago
- PRISM is a software for split read (reads which span across a structrual variant -- SV...duplications with the direction of discordant read pairs. PRISM_CTX is a tool fo...nal information is available in the PRISM README file and PRISM_CT...
2697 days ago
- ...h-quality scaffolds from NGS data (reads and contigs). The tool is wr...ner in case one needs to first map reads to contigs (instead of provi....sam files produced after mapping reads to contigs and the resulting...ile(s) corresponding to the second read of the read pair; -i)...
2694 days ago
BIMA V3: an aligner customized for mate pair library sequencing
...mal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome i...introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contaminati...2693 days ago
- ..., memory-efficient and highly accurate pair-end read merger. It is fully paralleli...memory. PEAR evaluates all possible paired-end read overlaps and without requirin...ementation, it can merge millions of paired end reads within a couple of minutes o...
2688 days ago
- PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format wi...mise the probability of the forward and reverse reads having come from a single pi...
2653 days ago
- ...and file parsing automatically via a simple GUI. Contig boundaries and read coverage can be displayed for...or even raw, unassembled sequence data. BRIG also accepts SAM-formatted read-mapping files enabling genomi...
2629 days ago
PBSuite: Software for Long-Read Sequencing Data from PacBio
...uite code found in downloads.----- PBJelly -----Read The Paper http://www.plo...automated pipeline that aligns long sequencing reads (such as PacBio RS reads or...upgraded draft genomes. ----- PBHoney -----Read The Paperhttp://www.biomedcen...2618 days ago
