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RNA Seq Basic Galaxy Tutorial RNA-Seq tutorial based on Trapnell et al. (2012) Nature Protocols In this tutorial we cover the concepts of RNA-Seq different...3636 days ago
- ...variants More at http://bioinform.github.io/breakseq2/ Download BreakSeq2 Latest version: https://github.com/bioinform/breakseq2/archive/2.2.tar.gzFor other versions, see "relea...
2971 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
...ed End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz...2926 days ago
Bpipe - a tool for running and managing bioinformatics pipelines
Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. January 20th, 2016 - New! Bpipe...2889 days ago
- LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. Publication: L. Salmela, R. Walve,...
2149 days ago
OPERA : Optimal Paired-End Read Assembler
...scaffolding large genomes (multi-library support, better repeat-handling etc.), in addition to other scalability and usability improvements (bam and gzip support, smaller memory foo...2779 days ago
- ...one by invoking make. Premature assembly processes can be resumed. Here is an example:run-fermi.pl -dAPe ./fermi -p NA12878 -t16 -f18 reads*.fq.gz > NA12878.makmake -f NA128...
2779 days ago
- SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Download Git repository of SWALO is at https://github.com/atifrahman/SWALO.
2697 days ago
- Minia is a short-read assembler based 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 conti...
2689 days ago
Standardized velvet assembly report
...attention to the kmer, cvCut, expCov, and other flags To Run: perl fastaAllSize mysequences.fa > mysequences.stat or gunzip -c mysequences.fa.gz | fastaAllSize > mysequenc...2688 days ago
