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Picard is a set of command line tools for manipulating high-throughput sequenc...ts are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification. Note that the informati...2978 days ago
- ...ebpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI). More...
2978 days ago
- ...Ion Torrent Solexa (Illumina) sequencing (in development) Pacific Biosciences sequencing into contiguous sequences (called contigs). One can use the sequences of differe...
3001 days ago
RACA: Reference-Assisted Chromosome Assembly
Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into lo...pubmed/23307812 http://bioen-compbio.bioen.illinois.edu/RACA/3001 days ago
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
...nt and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a fe...g the target fragment size as input. In addition, it implements a statistical test for minimizing false-po...3001 days ago
QUAST: quality assessment tool for genome assemblies
QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple asse...3001 days ago
REAPR: a universal tool for genome assembly evaluation
...a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds...new broken assembly based on the error calls. The software requires as...umina library is also available, REAPR can combine this with the large...3001 days ago
- SCALCE (/skeɪlz/, a.k.a. boosting Sequ...ompression Algorithms using Locally ConsistentEncoding) i...sing FASTQ files. It is designed specifically for the Illumina-generated...e at http://sfu-compbio.github.io/scalce/
2992 days ago
- Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC co...
2992 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
...30:10) Remove leading low quality or N bases (below quality 3) (LEADING:3) Remove trailing low quality or N bases (below quality 3) (TRAILING:3) Scan the read with a 4-base wide...2992 days ago
