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.1395 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...1096 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...1158 days ago
831 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...825 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...706 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.419 days ago