Background The accuracy of transcript quantification using RNA-seq data depends on many
factors, such as the choice of alignment or mapping method and the quantification model …

Sequence-level searches on large collections of RNA sequencing experiments, such as the
NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the …

… The authors wish it to be known that, in their opinion, Fatemeh Almodaresi and Hirak Sarkar
… (a–c) We compare the F-1, spearman correlation and mean absolute relative difference …

The colored de Bruijn graph— a variant of the de Bruijn graph which associates each edge (ie,
k-mer) with some set of colors — is an increasingly important combinatorial structure in …

The colored de Bruijn graph (cdbg) and its variants have become an important combinatorial
structure used in numerous areas in genomics, such as population-level variation detection …

Motivation Sequence alignment is one of the first steps in many modern genomic analyses,
such as variant detection, transcript abundance estimation and metagenomic profiling. …

… to Ω ( f j ) as the label of f j for all f j ∈ F q ⁠, where F q is the equivalence class to which f j
belongs… We define two fragments f m and f n to be equivalent (⁠ f m ∼ < f n ⁠) if and only if Ω ( …

… To compute Pr(f j | r i ), we evaluate the compatibility of fragment f j with the reference r i by
considering the alignment score computed by PuffAligner [69]. Furthermore, we also consider …

… entry to F per k-mer in the input. Note that we do not need to sort list of items in F completely—we
need only uniquify it. Assuming we have, say, O ( n ) memory, we can partition F into n …

… Fragments f i and f j belong to the same equivalence class if M ( f i ) = M ( f j ) ⁠, where M ( f i
… of transcripts to which fragment f i maps, and M ( f j ) is the set of transcripts to which f j maps. …