Results for "sam"
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...ing on the amplicons types (ITS or 16S). If WGS are chosen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads...2712 days ago
- ...rst map reads to contigs (instead of providing .sam files). The arguments accept...y where ScaffMatch files are stored. These are .sam files produced after mapping...-1) (Comma separated list of) either .fastq or .sam file(s) corresponding to the...
2700 days ago
- ...draft genomes or even raw, unassembled sequence data. BRIG also accepts SAM-formatted read-mapping files...bling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneo...
2635 days ago
splitbam: splits a BAM by chromosomes
...onary (*.dict), it also 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...itbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin) Options -h help; T...2623 days ago
- Samtools is a suite of programs for interacting...It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReadin...ing/writing high-throughput sequencing data Samtools and BCFtools both use HT...
2608 days ago
- ...d strains or serovars. Comparing gene expression values across multiple samples or timepoints. Visualizi...d datatypes and file formats: BSR and TRF output, SAM/BAM files, VCF-enco...
2505 days ago
Biological file format tutorial
...inguish the difference between different formats. Please refer user manual or other information resources on web for more details. FASTA FASTQ SAM BAM VCF GFF GTF...2330 days ago
CrossMap: a program for convenient conversion of genome coordinates
...s Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/...2166 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
...gns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5...2173 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...-a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and...map2 -a MT-human.mmi test/MT-orang.fa > test.sam # use presets (no test data)...nimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-e...2146 days ago
