Results for "SAM tool"
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maftools - An R package to summarize, analyze and visualize MAF files. Intr...s seqenced over 30 different cancers with sample...as long as the data is in MAF format. Maftools can also handle ICGC Simple Somatic Mutation format. maftools is on bioRxiv Please cite...2645 days ago
- BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular...n raw, unassembled sequence data. BRIG also accepts SAM-formatted read-mapping files...s present in unassembled sequence data from multiple samp...
2644 days ago
- GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rea...
2644 days ago
- Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific...
2644 days ago
- Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmeti...ED, GFF/GTF, VCF. While each individual tool is designed to do a relativel...
2637 days ago
FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.2634 days ago
PBSuite: Software for Long-Read Sequencing Data from PacBio
PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The Paper http://www.p...2634 days ago
splitbam: splits a BAM by chromosomes
...creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash. Usage java -jar...M__/__CHROM__.bam -R ref.fasta (bam|sam|stdin) Options -h help; Th...2633 days ago
Laj: viewing and manipulating the output from pairwise alignment programs
Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of...2632 days ago
- A computational pipeline for identifying single-base substitutions between two clos...ded to determine small insertions/deletions. Our main motivation is to use this tool to survey the genetic diversi...
2632 days ago
