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Maq: Mapping and Assembly with Quality
...riants and evaluate the results in one go: maq.pl demo ref.fasta calib-30.dat where calib-30.dat is contained in maq-data. View the alignment: cd maqdemo/easyrun; m...2782 days ago
- ...ds used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified refer...
2779 days ago
- ...t data manipulation (mostly genomic sequences, alignments, variation etc.), as we...ious analyses. It also features three sequence alignment packages: Satsuma,&...and SLAP, a context-sensitive local aligner for diverged sequences wit...
2776 days ago
- ...all the assemblies of the partition (using velvet with kmer value of 31). 5. Finaly, re-assembling the whole dataset with the merged contigs or the combined contigs, using a given kmer size. h...
2775 days ago
- ...amplicons types (ITS or 16S). If WGS are chosen, 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...
2773 days ago
- ...on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de...
2766 days ago
Standardized velvet assembly report
...t2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate alignments against a reference gen...ermute.sh mysequences (leave out the .fa) https://github.com/leipzig/standardized-velvet-assembly-...2765 days ago
- ...eters of velvet, and the process involved in producing a de novo assembly from Illumina reads. http://evomics.org/learning/assembly-and-alignment/velvet/
2765 days ago
- ...direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events. PRISM and PRISM_CTX were originally designed and written by Michae...
2764 days ago
- Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimm...
2760 days ago
