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Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are thre...data. If amplicons are input data, then bipype does reconstruction and pairs...biodiversity is searching. There are two types of searching depending on th...2768 days ago
- ...cy codebase) For the impatient A typical Minia command line looks like: ./minia -in reads.fa -kmer-size 31 -abundance-min 3 -out output_prefix Type ./minia for a quick explana...
2761 days ago
- ...tation of DNA sequence reads. More at https://github.com/jts/sga SGA dependencies: -google sparse hash...oogle.com/p/google-sparsehash/) -the bamtools library (https://github.com/pezmaster31/bamtools) -zlib (htt...
2761 days ago
- ...ke 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 case, it is advisabe to specify the format of the data pr...
2761 days ago
Standardized velvet assembly report
...pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLA...our PATH. If using BLAST, add blastall and formatdb. Edit permute.sh to your liking, payin...2760 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...
2755 days ago
Understanding Greedy Algorithms
...eedy-is-good/ This webpage is also useful for the same: http://learninglover.com/examples.php?id=59 http://www.cs.rpi.edu/~magdon/ps/conference/super_biokdd.pdf https://ocw.mit....2757 days ago
- ...hing able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case o...
2756 days ago
CISA: Contig Integrator for Sequence Assembly
...ler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate t...rial genomes. A tool, named CISA, has been developed to integrate the assemblies...2754 days ago
MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation
MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requir...prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de novo as...2754 days ago
