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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...2624 days ago
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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...2331 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/...2167 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...2174 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...2147 days ago