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Maq: Mapping and Assembly with Quality
...ce (ref.fasta). Better a bacterial genome. Download maq, maq-data and maqview at the download page. Copy maq, maq.pl and maq_eval.pl to the $PATH or to the same directory. Si...2736 days ago
Standardized velvet assembly report
Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part o...ference genome). If using BLAT, add faToTwoBit,gfClient,gfServer to your PATH. If using BLAST, add blastall...2719 days ago
MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
...e user-declarable at runtime. It is written to run on Linux. Requirements: You will need to have the following tools installed and in $PATH, or added to $binpath in the tool: Newbler (specif...2709 days ago
- ...NT NOTE: Progressive Cactus does not presently support installation into paths that contain spaces. Until this is resolved, you can use a softlink as a workaround: ln -s "path with spaces" "installation pa...
2680 days ago
YASRA: Reference based assembler
...Please install LASTZ (the newest version on http://www.bx.psu.edu/~rsharris/lastz/newer) and add the LASTZ binary in your executable/binary search path before installing YASRA....2637 days ago
MIX: Combining multiple assemblies from NGS data
...existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that m...2204 days ago
- ...gorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes...
2181 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...ogy, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence...2100 days ago
Synteny and Rearrangement Identifier (SyRI)
...(WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear reg...1476 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA d...1467 days ago
