SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
...utpus alterred contigs in FASTA files, spiked-in variants in VAR files (see Manual), simulated short read in FASTQ files and aligned short reads in BAM files.1405 days ago
CoverM: Read coverage calculator for metagenomics
... coverm genome (help) or individual contigs coverm contig (help). Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or...1105 days ago
FiNGS: Filters for Next Generation Sequencing
Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully use...1167 days ago
840 days ago
CrossMap: program for genome coordinates conversion between different assemblies
...bsp;different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wi...834 days ago
Quip: Aggressive compression of FASTQ, SAM and BAM files.
...fer times Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing lar...716 days ago
ALE: Assembly Likelihood Estimator
Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.428 days ago