Results for "bam"
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ZENBU: a collaborative, omics data integration and interactive visualization system
...ng and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files....1942 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
...d contigs and the correct, unaffected contigs. https://nxrepair.readthedocs.io/en/latest/tutorial.html nxrepair aligned_matepairs.bam assemblyfasta.fasta error_loc...1922 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as woul...1626 days ago
- Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polis...tput the polished and aligned sequences in a bam file via the option --ou...s.vcf -o polished_variants --output-polished-bam
1590 days ago
MGSE: Mapping-based Genome Size Estimation
...Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads...64-018-5360-z) allows the generation of a COV file based on the (sorted) BAM file (also possible via MGSE...1564 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments. More at&nb...1553 days ago
- Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape ca...
1543 days ago
SeqMule: Automated human exome/genome variants detection
SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.1532 days ago
pbmm2:A minimap2 frontend for PacBio native data formats
...ameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbm...1532 days ago
tinycov: standalone command line utility written in python to plot coverage from a BAM file
Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plo...1498 days ago
