Results for "BAM"
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TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as inpu...2288 days ago
CrossMap: a program for convenient conversion of genome coordinates
...man hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF,...2170 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM for...2177 days ago
WhatsHap: fast and accurate read-based phasing
...g et al., Read-Based Phasing of Related Individuals). WhatsHap is easy to install It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF....2173 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...nd view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data...2141 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
...ence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web brows...2102 days ago
SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
...be used for any dataset which can be expressed as a series of genomic positions. It's main features are: Import of mapped data from mapped data (BAM/SAM/bowtie etc) Creation of...2067 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generat...files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it wo...2043 days ago
AMStat: display statistics of large sequence files from next generation sequencing projects
...is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are...2008 days ago
BamView: a free interactive display of read alignments in BAM data files
...le run the UNIX: java -mx512m -jar BamView.jar and extra command li...given when '-h' is used: java -jar BamView.jar -h BAM files can be...the '-a' option: java -mx512m -jar BamView.jar -a pathToFile/sorted....in the viewer. To make this easier BamView will read in files that c...2008 days ago
