- BAM FILE FORMAT DECOMPRESSION SOFTWARE
- BAM FILE FORMAT DECOMPRESSION CODE
- BAM FILE FORMAT DECOMPRESSION LICENSE
- BAM FILE FORMAT DECOMPRESSION TORRENT
However, the tools for generating the CRAM formats are not designed to handle the flow signals. Compressing SAM/BAM into CRAM format significantly reduces the space needed to store the NGS results. The flow signals occupy a big portion of the BAM file (about 75% for the human genome).
BAM FILE FORMAT DECOMPRESSION TORRENT
In addition to the usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data.
BAM FILE FORMAT DECOMPRESSION SOFTWARE
The built-in software for the Ion Torrent sequencing machines delivers the sequencing results in the BAM format. Project description:BACKGROUND:Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. It is released under an MIT licence and available for all platforms on Bioconductor (, last accessed February 22, 2021) and on Github (, last accessed February 22, 2021). sangeranalyseR supports the use of colorblind-friendly palettes for viewing alignments and chromatograms. sangeranalyseR comes with extensive online documentation and outputs aligned and unaligned reads and contigs in FASTA format, along with detailed interactive HTML reports. Input data can be in either ABIF or FASTA format.
sangeranalyseR provides a wide range of options for all steps in Sanger processing pipelines including trimming reads, detecting secondary peaks, viewing chromatograms, detecting indels and stop codons, aligning contigs, estimating phylogenetic trees, and more. It also provides complete flexibility for determining how individual reads and contigs are processed, both at the command-line in R and via interactive Shiny applications.
BAM FILE FORMAT DECOMPRESSION CODE
It allows users to go from loading reads to saving aligned contigs in a few lines of R code by using sensible defaults for most actions. Project description:sangeranalyseR is feature-rich, free, and open-source R package for processing Sanger sequencing data.
BAM FILE FORMAT DECOMPRESSION LICENSE
The software is freely available at a General Public License (GPL) license.Our method requires having different reference genomes and prolongs the execution time for additional alignments.The proposed multi-reference-based compression algorithm for aligned reads outperforms existing single-reference based algorithms. The proposed approach achieved 15% more storage savings over CRAM and comparable compression ratio with Samcomp (CRAM and Samcomp are two of the state-of-the-art genome compression algorithms). The lossless compression can be produced by setting k (the number of clusters) to the number of different quality values.The proposed method produced a compression ratio in the range 0.5-0.65, which corresponds to 35-50% storage savings based on experimental datasets.
The lossy compression mechanism for the base quality values uses k-means clustering, where a user can adjust the balance between decompression quality and compression rate.
Regarding the base quality value, we offer lossy and lossless compression mechanisms. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read length. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data.We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. Project description:Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease.